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.
Other mistake: During a flashback, Rogue is shown absorbing Pyro's mutant power and then creating fire out of thin air. However, Pyro does not have the ability to create fire, he can only control it. That's why he wears a flamethrower on the back of each hand.
The Unstoppable Juggernaut - S1-E8
Continuity mistake: Gambit is the central character in the previous episode "Slave Island", and is on the Blackbird with the rest of the team when they arrive at the destroyed X-Mansion. However, the very next episode begins where "Slave Island" left off, and Gambit is conspicuously missing from the episode.
No Mutant Is an Island - S5-E4
Character mistake: When Cyclops demonstrates his power to Rusty to show him that he's also a mutant, he shoots an optic blast at a building and blows a gigantic hole in its facade. While the building had the appearance of being condemned, Cyclops had no way of knowing whether there were squatters inside. He could have seriously injured or killed several people for all he knew. (00:07:35)
Savage Land, Strange Heart (1) - S3-E8
Character mistake: When Zaladane is placing the Garrok necklace around Karl Lykos' neck, she incorrectly refers to Garokk as "Garokkt." She's Garokk's high priestess, so she should definitely know his name. (00:04:12)
Savage Land, Strange Heart (2) - S3-E9
Other mistake: When Rogue tells Beast that the word "Zaladane" kept popping in and out of her head when she and Sauron made physical contact, a border roughly in the shape of the letter "D" appears around her mouth. (00:08:08)
Factual error: At the end of the episode when Carol Danvers is shown comatose, there is an EEG machine next to her bed. This machine monitors brain activity and uses electrodes on the patient's head in doing so. She has no electrodes placed on her head, and the machine isn't detecting activity in her brain. (00:20:37)
The Phoenix Saga (4): The Starjammers - S3-E6
Other mistake: When D'Ken is saying "Destroy them all," he is speaking with a German accent. (00:17:09)
The Phoenix Saga (3): Cry of the Banshee - S3-E5
Other mistake: When Xavier is telling Moira about how he and Lilandra were attacked, Moira dismisses his claim, reasoning that he came to her for help because he could no longer trust his own mind, and that no-one else had been in his room. She witnessed him flying out of a window, and he's a paraplegic. Unless she thinks he somehow catapulted himself out the window, she shouldn't have been so dismissive of his claim. Not to mention the damage to the room, including the bed being thrown against the TV. (00:05:21)
The Phoenix Saga (1): Sacrifice - S3-E3
Other mistake: When Dr. Corbeau opens the door to the locker room, Cyclops, Jean Grey and Wolverine are in his direct line of sight. Despite this, it isn't until he takes several steps into the room that he realises they aren't his shuttle crew. (00:08:35)
Other mistake: After Magneto says "Trust me, you'd rather not know," a hole appears in his pants around his right hamstring and then quickly disappears. (00:02:50)
Other mistake: When Xavier asks Magneto how much further they have to reach the top of the cliff, Magneto tells him he would rather not know, suggesting they still have a long way to go. However, in the wideshot of the sky-riders flying in to attack the two, you can see Magneto is about three times the length of his own body from the top, and according to the book "X-Men: The Art and Making of the Animated Series," Magneto is 6 feet tall. This means he is only about 20 feet, give or take, from the top, which isn't all that far in terms of climbing a cliff. (00:02:44)
Character mistake: When wondering how close they are to the top of the cliff, Xavier asks Magneto "How much further?" The word "further" is used for non-measurable or figurative advancement. He should have asked how much farther, as that refers to actual distance between objects. An educated man like Xavier would certainly know the difference between the two. (00:02:44)
Suggested correction: While "farther" is used for physical distance, further can be too, especially in British English. Farther also tends to be used for a measured physical distance, so if the actual distance isn't known, further can be used. What Charles said is grammatically correct.
Mojovision - S2-E11
Revealing mistake: When the X-Men are being returned to the electronics store, there is a noticeable jump-cut (odd for a cartoon) just before Wolverine materializes. (00:18:40)
Mojovision - S2-E11
Revealing mistake: When the Gladiator robot shoots an optic blast at Wolverine, you can see the hole in the chest area of Wolverine's uniform is already there before the blast hits him. (00:16:24)
Mojovision - S2-E11
Revealing mistake: When Mojo's studio audience is cheering after he says "I give it two flippers up," you can tell by each character's celebratory movements that it is just a reverse of the shot where the audience was first shown earlier in the episode. (00:07:50 - 00:15:23)