If Danny had no memory of his powers, Sam shouldn't have gotten the Fenton Thermos when fighting Nightmerica. However, she could have taken it at Danny's basement (when he regained his powers) when she went to fight Desiree.
When Desiree confronts Danny in the water fountain, just after Danny goes ghost, you can see that he is bobbing up and down as though he were floating. In the shot directly before and directly after this, you can clearly see that his feet are in the water and touching the bottom on the fountain.
When Danny is looking through Sam's scrapbook when she is trying to convince him that she is his best friend, he is flipping the pages the wrong way (left instead of right)
When there's a close-up of Sam's face as she says "I gotta.", the pink lipstick and blush she was wearing are missing and she is wearing her regular purple lipstick instead.
In theory, the Fenton Thermos shouldn't have worked at all until after Desiree returned ther memories. In the first episode "Mystery Meat" when Danny traps the Lunch Lady, he is clearly seen to somehow charge up the Fenton Thermos with his ghost energy to get it to work; but since Sam had wished he had never met her, he would have never gained his ghost powers and therefore been unable to activate the thermos.
During Danny's fight with Femalien, they land in what appears to be a storage room or an office. However, in one shot, Lancer's desk and the chalkboard from Mr. Lancer's classroom are clearly visible. However, in the shots afterwards, it once again appears to be a storage room.
When Spectra spins Danny (on a stretcher) towards the "DNA extractor machine" his eyes are momentarily green - in his human form. Then they turn blue again.
When Sam screams and Danny comes in, there is a moving medical meching in the background. Sam doesn't have any thing attached to her so it shouldn't be moving. When Danny puts Sam back in the bed after she involuntarily floats up, the machine is gone.
When Danny is on the stretcher, it shows him looking around. It shows his feet and there is clearly no restraint, just an ectoplasmic energy glow.
When Paulina opens her locker door, there is a picture of Phantom on the side where he doesn't have his entire glove. In the next shot where a ghost bug lands on Paulina's hand, Phantom is wearing his entire glove.
When Spectra pins Danny to the ground with her foot and the Jack snot DNA is kicking in, it pans up to show her gloves missing. Once she gets off Danny for the countdown to power, the gloves are back.
In the opening sequence where Vlad tries to steal Pariah Dark's Crown of Fire, it is on his head, who is in the sarcophagus, but in the flashback, the seven ghosts are seen taking his crown off before putting him in the Sarcophagus of Forever Sleep.
When Vlad goes to steal the Ring of Rage and Crown of Fire, the wall to the sarcophagus is open. When Danny goes to fight Pariah, he has to destroy the wall to reach the sarcophagus. Although it is possible that Pariah or the Fright Knight sealed the wall previously, or it could be that Danny and Pariah were fighting in a different room.
Technus appears briefly in this episode in his form from "Teacher of the Year" despite still being trapped in the "Doomed" video game until the next episode, "Identity Crisis".
When everyone is arguing about who should wear the Ecto-Skeleton, Maddie is seen with her hood off before she is knocked out. Seconds later, when the screen shows everyone unconscious, she has her hood on.
When Vlad transforms back after being defeated by Pariah the first time, his ring disappears as he becomes his Masters form. Likewise, while the ring was in his right hand, he later clutches it in his left in the next scene he appears.
There are six Ancient Ghosts at the beginning of Skulker's story, but seven by story's end.
After Danny beats Pariah, the Skeleton Fighters poof into thin air, yet a news broadcast says that residents are continueing the cleanup and they show a trashcan full of bones.
After Skulker's story, Ember mentions that Pariah had already destroyed their homes. Danny remarked that he did that without the Ring of Rage. When it cuts to a close-up on his head for when he says that they have to keep the Ring from him, he has no ghostly glow.
This episode shows that Technus has been trapped in the "Doomed" video game ever since "Teacher of the Year." This means his appearance in "Reign Storm" is likely a goof.
When the Ghost Catcher was first shown in the episode "What You Want", Ghost Danny is able to rejoin with Human Danny again without any extraneous effort; however, in this episode, when Super Danny tries to fuse with Fun Danny, the latter merely gets overshadowed by the former. This may indicate that the effect becomes stronger after some time, or simply that the effect can vary.
When Danny splits himself, his ghost half's hair and cape constantly wave as if there was wind - even when there's no wind at all.
After Danny deletes "Doomed" In the background of Technus it still says the game is there.
When Valerie gets hit by the Fright Knight, she does not have any bruises. But later when she falls to the ground, she is seen with them. It may be that she didn't get the bruises from the blast but from the landing.
In the first shot of Dark Danny cheating on the Career Aptitude Test, it is misspelled as "Careear Aptitude Test".
When Clockwork shows what's about to happen to the observants, right after he gives the answers to Danny, we can see a scene where Danny fights Dark Danny, whose beard is black and not white.
Clockwork's medallions disappear and reappear throughout various scenes and from characters when they're supposed to be constantly worn (Such as Skulktech 9.9 not seen wearing one until it falls off). Surprisingly, Danny did not return to his time whenever Dark Danny removed his medallion to fuse him with it (though it may have been because Dark Danny was in contact with both him and the medallion, as the temporal effects seem to extend to people in physical contact, otherwise, Skulktech could not have brought them with him when he went back to Clockwork's lair).
When Danny is fighting Dark Danny for the 2nd time, he puts the Spector Deflector on him, but amazingly the gloves stay on the belt when he lets go.
When Dark Danny fuses Clockwork's time medallions into Danny, it remains in his hand after he puts it inside Danny when it shouldn't.
A close-up on Danny's face when he says, "Time's up!" shows him in his ghost form (with white hair and green eyes), even though he was forced out of it (by using his ghostly wail) a moment before. In the shot immediately afterward, (when he uses the Fenton Thermos on Dark Danny) he is in his human form.
At the beginning, Dark Danny destroys FentonWorks completely, but later on when Danny, Sam, and Tucker end up in the future, right before Sam and Tucker go back in time, the building is still there, Considering the Ops center still retains the crack in the middle as it did earlier, it could've merely been re-built.
When Vlad is telling Danny about the death and how he came to him. When Danny looks at the picture of his family and friends it is taken in front of Fenton Works:
In the picture, it just says Fenton.
In the picture, Sam has pupils.
In this episode, the Ghost Gloves from episode 5 are changed to the Ghost Gauntlets. It's not shown how Vlad managed to get them.
When Danny's family and friends are first shown to be killed by the explosion:
Danny says "No!" after the explosion, but when the real events occur near the end of the show, he says it before the explosion, though it could most likely be because he knew it would happen.
The form of the explosion is similar to the form of an atomic bomb explosion, but once Dark Danny is captured, the form is more of an outward explosion.
When Danny and Clockwork go back in time to CAT testing by the end by two hours early, the clock shows that it's five to nine despite Lancer asking to meet the Fentons at 5PM.
When Clockwork says, "You must be eliminated before you permanently alter the timestream." he is in his old form. Immediately afterward (when he makes other versions of himself appear), he is in his adult form. Right after that, he is in his old form again.
When Clockwork takes Box Lunch to the past, his scar on his face switches from his left side to his right.
When Vlad tells Danny about what happened to his friends and family the front page of the newspaper has a picture of the Nasty Burger totally wiped out by the explosion, although in the future scenes and immediately after the explosion at the end of the episode parts of the building remain.
Dark Danny duplicates himself into four copies to fight Danny. But after he overpowers the present Danny, Dark Danny is seen with five copies instead of four.
When Danny, Sam and Tucker first go to the future and Valerie traps Danny in a ghost net, you don't see his colors. But when they first meet Dark Danny (after the commercial break) you can see the colors through the net (which were not visible before).
Dark Danny's ponytail is flaming in some parts of the episode along with the rest of his hair and sometimes, it's completely motionless.
After Danny uses his ghostly wail for the first time when he changes back only his head changes. (Though this might be because of the time medallion or because it was his first time using it, so it wasn't as powerful and didn't drain him as much, so he only partially reverted back.)
Just before Danny catches the flag pole, he is seen with green eyes while he is in his human form.
At the end of the episode when the Observants are reprimanding Clockwork, the Fenton Thermos containing Dark Danny is missing the lid.
When Sam discovers the screen showing Danny's future, she brings the boys over to see it. In the scene where law enforcement tries to come close to Dark Danny, he has no DP logo on his suit.
When Danny turns away from the fire after the oil tank explodes during his second fight with Dark Danny, the former has no ghostly glow (though it could be because of the light of the fire).
After Dark Danny grabs Danny with his ectoplasmic rope, Danny is seen without his backpack for a few shots before it later returns.
As Danny punches Dark Danny into the oil truck, Dark Danny seems to be seen without the specter deflector on his waist, returning when he is next seen.
During Danny's transformation, after the ghosts arrive in Amity Park, his white rings appear to be frozen.
At the end, as the ghosts help Danny, Spectra is seen in both of her forms: her shadow ghost form and her modified form from Doctor's Disorders — she is even seen picking up Christmas trees twice, in a different form each time. Incidentally, Technus is seen in both his normal and 2.0 form as well.
When the main trio brings in a Christmas tree to the little boy's house, Sam's jacket can briefly be seen as red, instead of black.
When Danny first goes ghost to find Jazz, he's in pajamas. After the fight with Vlad, on the way home though, Danny is seen in his regular clothes.
When Jazz is searching Danny's ghost files, she complainingly asks to Danny why didn't he tell her about Vlad's ghost powers and about his "thing" on Maddie. However, in "Bitter Reunions", Jazz is clearly informed by Danny about the second fact shortly after they first meet him, when Danny (who still didn't know about the ghost powers) asks Jazz if Vlad was hitting on their mother, but she barely ignores it.
A running gag occurs with Jazz and a Fenton thermos - causing everything to go wrong and captures Danny instead, even though in "My Brother's Keeper" she uses the thermos without a problem.
When Tucker was laughing at Danny about being crammed in the Fenton Thermos, Dash stuffs Tucker in his locker. Then Danny is seen leaning on Dash's locker while Sam is cracking the lock on the one next door to Dash's. Somehow Tucker had switched lockers from the one Danny was leaning on to the one next to it.
When Danny and Jazz were leaving Vlad's stadium, Jazz is seen with a ghostly glow.
When Vlad comes out of his lab after Jazz claims she will be scarred forever by his Maddie photos, his hair's color and the color of the line across his hair are momentarily swapped. His main hair was grey and his line was dark grey instead of the usual vice versa.
When Danny remerges after the axe ghost slices him his eyes shortly flicker.
Although Danny claims he never could split himself up like Vlad, when fighting the axe-wielding ghost he splits in two to avoid being cut in half, but he doesn't pay any attention to it and the halves fuse together. This could have been a reflex.
When Aragon throws a rock at Danny, his ghost self is intangible, but since he is in the ghostzone he should have been hit.
Although Sam's hair is only chin-length, it's impossibly long when she puts it in ponytails.
Dora says that Aragon has been picking on her for 1600 years, but seeing as this episode is set in 2006, 1600 years ago would be the fourth century. That's 200 (or 600 with the Dark Ages) years earlier than the Medieval times. The Knights are dressed in 14th century armor and the clothes that they wore and the others in their realm are that of the 13th century. So when are Dora and Aragon from? Dora could simply exaggerated in a fit of anger.
After Lancer tells the students the legend of the king returning when the right reflection appears in the sacred mirror, he walks past it without any reflection.
Frequent times during the episode, Hotep-Ra's uncovered eye switches from left to right.
Mirrors didn't exist until the 19th century, but to revive Hotep-Ra the lengend says that the Pharoah's reflection must be shown. Either the legend was created after the creation of mirrors, or the writers didn't check when they were created. Glasses also weren't invented until the 13th century, so it is possible this was added to make the Pharoah look more like Tucker.
When Clockwork sends Danny into the past he is able to exist freely in both the past and alternate future without wearing a time medallion, even though in "The Ultimate Enemy" Clockwork explains that the only way to exist in a different timeline (that isn't your own) is by wearing one.
When Jack Fenton is first shown after Danny changes the timeline, he has his normal present-day hair-do, but when Jack transforms out of his ghost mode in front of Maddie near the end, his hair goes back to how it was when he was in college.
When Danny is first shown wearing '80s clothes, the cuffs on his sleeves are black. When the cuffs shown again, they're white.
When Maddie sucks Danny into the "Maddie Weasel," he wakes up later on a table still in ghost form, even though every other time he passes out in the series, he turns back into Danny Fenton.
When Jack became a ghost, his ghost energy blasts was green but when he was about to hit Danny before Danny held up the piece the newspaper, his hand glowed pink.
Towards the end of the episode, Sam is talking about, "No fifteenth birthday." In one shot she is being tended to by Jazz. In the next, Sam is cared for by Maddie.
Dani's jumpsuit will sometimes have a white ring around the neckline and sometimes not throughout the episode.
When Dani first reveals her powers, there is a similar error to Danny's first revealing of his powers. Once her upper midmorph ring reaches her liver area, her suit is already fully formed but she still has yet to change her eyes to green.
Additionally, once she is fully ghost she has no ghostly glow. In the next scene, she does.
When Danny's listing off the things Gregor has in common with the Guys in White, one of the items is that they both have white hair. However, the Guys in White are bald.
When Gregor smells Sam's hand, for one moment, you can see his eyes are grey. However, at the end of the episode, his eyes are clearly green.
When Sam and Gregor are at the mall food court sharing a plate of spaghetti, the scene opens with Sam on the left and Gregor on the right. When it cuts back them later, Sam is on the right and Gregor is on the left.
When Tucker, Sam, and Gregor are at the observatory, Tucker says, "Cool, it's a new moon." However, a full moon is shown right before his line, plus it's physically impossible to have a new moon at night since they occur during the day when the moon is between the sun and Earth (and thus can't be seen).
Just before Jazz bumps into Danny shortly after the title card and/or commercials, his eyes seemed to be grey. This also happened just before Danny says "3 to the Op Center" while in his house being chased by the Guys in White.
At the end of the movie, Danny states that only Sam, Tucker, and Jazz remember that he is half-ghost. But in future episodes it is clear that Vlad, Walker, Skulker and others know who he is. This could be because they were in the Ghost Zone at the time and Danny and Freakshow only used the Gauntlet to alter the human world. Or it could be that they knew he was a halfa beforehand, and that Danny was referring to the people who found out during the course of the episode.
In the title page where the faces of Danny, Sam and Tucker are seen in the reality gems, none of the characters correspond with the gem they hid.
The Gem of Life is not shown on the Reality Gauntlet during the title card. Not even the band for it is featured.
When Freakshow takes off his earring, he has one left. In the next shot, he has 2, then 1, then none at all, and for the rest of the movie, he has 2 earrings.
The Reality Gauntlet switches between having 3 or 4 bands for the gems, and the order of the gems change.
When Freakshow takes the Reality Gems out of the Fenton Thermos, you can see that it opens like it has a hinge. However, in every other episode and several times in this one, it doesn't have one.
When the space shuttle falls, it falls parallel to the ground. When they show it in the next scene, it's angled toward Sam and Tucker.
The Auto-Jack normally smiles showing teeth, but in the last shot showing him, he shows no teeth.
Although Freakshow wears the Reality Gauntlet on his right arm throughout most of the movie, when he's talking to Danny, Sam, and Tucker on the plane, he doesn't have the glove on.
When Danny goes ghost for speed purposes at the beginning of the episode, his midmorph ring forms right under his knees so they can be shown onscreen. When it splits and they pass over his.. genitalia, he is already completely in Phantom mode. Even then, the rings continued to spread.
Also, both of the rings go up when one of them should go down.
Ghostly glow goofs:
When Freakshow was granted permission to try on the Reality Gauntlet by the Guys in White at the beginning of the episode, his "ghostly" glow spreads to the Gauntlet. Sometimes it is appropriate for glows to spread, but in this case it happened before Freakshow even touched the Gauntlet so there's still partial inconsistencies.
Freakshow glows just like ghosts in this episode, despite being a human. Also, note that in "Control Freaks", he didn't glow. But he had spent the past months in prison with the Guys in White as his warden(s), so who knows what could've happened to him?
When Freakshow activates the Gem of Form for the first time & uses it to make those robots made out of train oil tanks, the robots already had glows despite just having new forms & not being ghosts at all yet; they were still just oil tanks and should've been until Freakshow uses the Gem of Life on them.
After the Reality Gauntlet explosion at the Dumpty Humpty concert, the drum spider turns back into a normal drum set but retains it's glow. In the next scene, it suddenly loses the glow and it stays like that from that point on.
While the Fenton Works defenses are protecting the trio as they run for the Op Center, there are times when it's weapons change from having glows to not having glows or vice versa.
When Danny is turning the Op Jet invisible, it has a glow except for the wings even before he manages to do it.
As Danny is shooting the spaceship with ghost rays after leaving the Op Jet, the spaceship's glow disappears until it roars.
When Danny is about to phase into the spaceship and take the Gem of Life, only his hair glows. When he throws up his arms to prepare for the phasing in, his hair's glow also vanishes. Then when he turns intangible, his entire glow comes back.
After Danny takes the Gem of Life from the spaceship and it turns back to normal, it's glow disappears as would seem reasonable. But in the second scene showing the ship falling, the glow is back. Right after that, it's gone again.
When Danny starts flipping switches on the row of green lights, his arm doesn't glow.
Another goof like that occurs seconds later. In the scene of Danny's legs pressing down on the spaceship's pedals, his legs didn't glow despite him being in Phantom mode.
The four wheelers Sam & Tucker rode on don't glow at most times, yet they do when they are in the 3rd scene of being used by Sam & Tucker to flee from the Guys in White at the space center. Additionally, their glows spread to the former at that moment.
While Danny is saying they don't need to destroy the stuffed animals at Gothapalooza, his hair seems to be the only thing on him glowing again.
When Danny phases the group out of the rocky hill near the road, he solidifies with them to show he's not glowing at all. In the scene right afterwards, he is.
Danny had managed to blend in with the geeks dressed as him, despite the fact that he's obviously the only one who actually glows.
Empress She-Wolf's normal form glows, but her even more wolf-like form doesn't. This might be normal, though.