Continuity mistake: When Magneto is telling Wolverine that Xavier wouldn't approve of his commando raid, his neck area is flesh colored, when it was previously shown to be purple because of his costume. (00:16:45)
Continuity mistake: When Shadowcat tells Iceman that Emma Frost knows what he is thinking, the shocked expression on his face is drastically more pronounced when the shot changes. (00:05:37)
Continuity mistake: When Emma Frost is lamenting her students being taken away from her, she is standing inches away from the window. A couple of shots later, and she has instantly moved several feet away from the window. (00:04:44)
Continuity mistake: When Magneto is standing at the foot of Xavier's bed, the bed frame and drapes are present or missing depending on the shot. (00:17:44 - 00:18:20)
Continuity mistake: When Magneto uses his powers to create a hole in the metal wall, the edges of the wall surrounding the hole are smooth. When the shot changes, the edges suddenly look crumpled. (00:17:16)
Continuity mistake: When the X-Men are following Magneto to see Xavier, Cyclops is on the far left and Iceman is standing next to him. Once Magneto has opened a doorway to the room Xavier is in, Cyclops and Iceman have swapped places. (00:17:10)
Continuity mistake: When Angel is saying goodbye to Wolverine, the driver's side door of his car is open, and he is standing on the interior side of it. When the shot changes, you can see the door is now closed (note the window glare). (00:03:41)
Continuity mistake: When Wolverine opens the door and Emma Frost is there, she is within less than an arm's reach of the door. When she says she has decided to join the X-Men, she along with Wolverine and Angel are suddenly a few steps outside away from the door, even though she was never shown stepping back. (00:02:17)
Continuity mistake: When Wolverine opens the door as Emma Frost is there, he is standing roughly two steps away from her. When he asks her why she's there, he takes a couple steps towards her and still only manages to be roughly the same distance away from her as he started. (00:02:17)