Continuity mistake: Rogue rips off Donald Pierce's cybernetic left arm, but when he is first shown running away, his right arm is the one that is missing. When he catches up with Sebastian Shaw in the secret passageway, his left arm is back to being the one missing.
Plot hole: After Storm's attempt to escape the Genoshan prison is thwarted, she ends up in the ocean right at the shoreline of the beach, where she is captured by a Sentinel. Aside from the fact that it makes no sense for a Sentinel to be hiding in the ocean in the event that a mutant tries to escape the prison, there is absolutely no way that a two-story tall robot could hide in the ocean right by the beach, as the water would be way too shallow. You can even see that the water level only goes up to the Sentinel's ankle area when it is standing upright in the ocean.
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.
Continuity mistake: Magneto straps Wolverine to the port side of a boat and then drops the boat on a warehouse. When Gambit is freeing Wolverine, Wolverine is suddenly on the starboard side of the boat. After Gambit frees Wolverine, they are both shown to be on the boat's port side.
00:17:00 - 00:18:00Phaneron
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.
Continuity mistake: When Cyclops blasts a hole in the floor beneath Sebastian Shaw and causes him to fall through it, Shaw lands on a catering table. Later when Beast jumps down the hole to attack Shaw, Shaw is emerging from underneath heavy rubble rather than a catering table, and he is inexplicably shirtless. The rubble also changes from being brown just before Beast jumps down the hole, and is then white after he lands. Additionally, the floor goes from being black-and-white checkered to a solid brown color.
00:15:55 - 00:17:05