Deliberate mistake: When the news program is discussing Gyrich's assassination attempt on Xavier from the series finale of the original animated series, he's shown to have his classic look of auburn hair and sunglasses. However, when this scene occurred, Gyrich had black hair and was not wearing sunglasses. This was done deliberately to match the character design of the original series prior to the final 6 episodes, when Saban took over and redesigned much of the show's look.
Snow Place to Go/Dunce Upon a Time/Gems the Breaks - S2-E4
Deliberate mistake: Dunce Upon a Time: When Lumpy falls off the beanstalk and hits the ground, his left antler is missing. Probably done deliberately so that his head could fall flat on the ground. (00:14:03)
The Defection of Hawkeye - S1-E8
Deliberate mistake: When Mandarin is watching and wondering why Julia is tailing Clint, the road surface and cliff walls around Julia's car are recycled repeatedly. (00:10:55)
The High Life / Best Friends - S2-E10
Deliberate mistake: In "The High Life", there is a scene where Stinky submerges his head in a tank of water. He delivers the line, "Gee willickers, it's still ticking", and everyone somehow understands what he is saying with his head underwater.
Suggested correction: Nobody responds to what Stinky says, so there's no reason to assume that everyone understood him.
Deliberate mistake: At Pete's diner, the owner puts the tray down, and instantly glasses appear in front of the 5 patrons. (00:02:50)
Deliberate mistake: When Fluttershy is telling off the cockatrice, her back legs and her wings turn to stone. But when she gives it the stare and the camera is right in her face her wings are outstretched.
Deliberate mistake: In this episode, it is revealed Donna and Robert got together because Robert saved her from a water fountain. In "Another Bad Thanksgiving", it was shown Donna's sister introduced Robert to Donna. (00:02:20)
Formidable Enemy!? Mother Coordinator Enters! - S7-E37
Deliberate mistake: This Pokémon Trainer's Choice segment incorrectly claims that Arbok evolves into Seviper, which isn't true. (00:11:38)
Deliberate mistake: When Thomas goes by the level crossing, a close up of Thomas is shown but it's the same footage from season 1, only flipped. Because of this, Thomas' number is mirrored.
Deliberate mistake: There's at least two episodes (Season 1's "Captive Hearts" and Season 4's "Sanctuary, Part 1") in which a character shows video footage of the X-Men and various supporting characters in action, but the footage is merely clips from previous episodes.
Deliberate mistake: As usual when the Hulk reverts back into Bruce Banner, he is left wearing nothing but tattered pants. When Mitch McCutcheon sneaks Bruce Banner into the nuclear research facility, Banner is shown wearing his usual outfit of a gray collared shirt tucked into purple slacks that are intact. Given that the Hulk was just in the middle of the Nevada desert, Bruce Banner would be in no position to have a change of clothes on him, and the idea that the top secret facility would have an exact match of his go-to outfit is ludicrous.
Winning Through Intimidation - S1-E15
Deliberate mistake: In the actual card game, attacking the castle ring would not be allowed, but this is probably done in order to enhance the show for kids.
Deliberate mistake: When the turtles and April escape the building filling up with water, the shot where the hall is filling up with water is used twice.
Deliberate mistake: When the sewer worker is trying to escape the Lizard, the fast lanes in both directions of traffic are visibly clear for several blocks, which is extremely unlikely in downtown New York. (00:01:10)
Deliberate mistake: There is a shot of Alexis getting blasted with electricity when Etoile Cyber is attacked by Sparkman. This same shot is reused later in the episode when she attacked directly by Elemental Hero Thunder Giant, as the electricity and Alexis' position in the shot is the same. (00:12:20 - 00:18:36)