Continuity mistake: When Magneto first notices the missiles being fired at Asteroid M, he is dressed in loungewear and Xavier is wearing his usual green suit. When the shot changes Magneto is suddenly wearing his costume and Xavier is wearing a more casual outfit. Given how fast the missiles are shown to be approaching, they wouldn't have had time to change their clothes. (00:15:45)
Continuity mistake: The missiles that are fired at Asteroid M are first shown to be approaching from Earth. When the shot changes, they are coming from the opposite direction. When the shot changes again, they are once again approaching from Earth. (00:15:45)
Continuity mistake: A crowd of people has suddenly gathered in front of Magneto when Xavier says he wishes to speak with him. (00:14:20)
Continuity mistake: When Gambit is trying to distract the Sentinels, both of his gloves are entirely fingerless whereas normally his gloves are only fingerless for the thumb, index and pinky fingers. (00:12:00)
Continuity mistake: When Magneto is showing Asteroid M to the delegates at the U.N. meeting, the Genoshan delegate he forced to sit down has either moved to another seat entirely or the people that were sitting around him moved to different seats and other people filled in their seats. (00:04:05)
Continuity mistake: When Magneto forces the Genoshan delegate to sit down, the chairs surrounding him are empty. A couple of shots later, the chairs are occupied. (00:02:35)
Continuity mistake: After Magneto crashes through the roof of the U.N. building, the nameplates designating the nations of the delegates have suddenly become blank. (00:02:20)