Other mistake: When the tank falls through the hole in the bridge, the tank's occupants are impossibly shown to be clinging to the edge of the hole at the same time the tank is going over the edge, as if the tank and the occupants were occupying the same space.
Other mistake: After Cable shoots his exploding plasma blast at the table that Gyrich, Trask, Hodge and the Leader are sitting at, the former three all evacuate the area while the Leader is still shown to be sitting at the table only a moment before it explodes, but he does not suffer any ill effects from the concussive blast or wooden shrapnel.
Other mistake: When Cyclops, Rogue and Jean Grey exit the War Room to depart for Genosha, at the top of the door frame there is a black spec moving around, possibly indicating that there was some debris or a clump of dust on the animation cells or the camera lens itself during filming.
Other mistake: When the hotel clerk is checking Gambit, Storm and Jubilee into their room, he determines that they are mutants by seeing footage of Storm using her powers at the Salem Center Mall from the very first episode. While it's not unreasonable that security footage from the mall could exist showing Storm use her powers, the footage also shows an extremely close zoom-in on Storm's left eye, which is extremely unlikely, unless the security camera somehow guessed she was about to activate her mutant powers.
Other mistake: When Storm sends the Genoshan prison guard flying into the Blob, he knocks the Blob over. The Blob's powers prevent him from being moved, hence why he is sometimes called the Immovable Blob. Other episodes demonstrated his ability to stand his ground against force, such as being punched by Rogue or being blasted by Cyclops' optical beam.
Other mistake: In the scene where Professor X uses his psychic powers to deduce that Jubilee is trying to escape the mansion, there is a semi-dissolve edit that simultaneously shows a close-up of Professor X with his left hand on his forehead and a counterpart image of Jubilee hiding around the corner. If you look closely at Professor X in the counterpart image of Jubilee, his left arm and hand are shown to be on his hover-chair's armrest and not his forehead.