Revealing mistake: When Quicksilver is fidgeting inside his containment shell, the animators neglected to properly sync his body movement. You can see that his shoulders are not "connected" to his arms, as if his head and shoulders were separated from the rest of his body.
Revealing mistake: When Mr. Sinister is mocking Jubilee, take a close look at his neckline as he moves his head. The animators moved his neckline as he moved his head, but his shoulders stay in place, so his head and neck look like they are floating above his shoulders.
Revealing mistake: When Warren's girlfriend is looking for him in his lab, she is startled by Cable who is hiding behind the door and slams it shut once she enters the room. When she is startled and looks back at Cable, the animation is not very fluid. As she is turning around to look at Cable, her "onion skin" form remains, making it look like there are two of her.
Revealing mistake: The shot of police cars surrounding Sabretooth and him throwing one of them into the air is a recycled shot of the very first shot in the series from the season 1 episode "Night of the Sentinels, Part 1." It's even revealed a few minutes later in the episode that this isn't actually Sabretooth, but a Phalanx facsimile that has taken his form, which makes the fact that Sabretooth's actions are being recycled all the more dubious.
Revealing mistake: After the New Men have captured Magneto, Wolverine, Scarlet Witch and Quicksilver, the establishing shot of the High Evolutionary's headquarters is a recycled shot of when Scarlet Witch and Quicksilver first arrived at his headquarters a few minutes earlier in the episode, played on a loop (note the lightning strikes and the High Evolutionary's pink energy field being repeated).
00:05:35 - 00:12:40Phaneron
Revealing mistake: The footage of Jubilee flying off in the mini-jet is recycled footage of her flying Colossus back to Russia from the season 4 episode "Red Dawn." You can even make out Colossus' silhouette in the window over the passenger seat in one shot, even though Jubilee is supposed to be by herself.
Revealing mistake: When Proteus is leaving his father's home while possessing the police officer, the green glow of his eyes doesn't stay in place as he is moving. You can see the green glows leave his face and float in midair with the eye slots on the face turning black. It appears that the animators couldn't keep the glowing eyes synchronized with the body movement.
Revealing mistake: When Professor X is telling Juggernaut that he is in his mind, if you look closely you can see there is a disembodied mouth on the right side of Professor X's face that is synchronized with his dialogue. Apparently an animation error.
Revealing mistake: After the X-Men rescue Dr. Corbeau and retreat back to the shuttle, they come upon a room with crew members passed out on the floor. Keep an eye on Wolverine in the background on the right side of the screen and you will see him literally walk through a door panel.