Continuity mistake: The length of the chain attached to the collar of Archangel's guard dog varies. When the dog is first shown, the chain is only shown to be around three feet long. When the dog discovers Psylocke, it is able to run several feet towards her and away from the wall where it was chained up.
Continuity mistake: The security footage of Cortez betraying Magneto is slightly different than the event itself. Cortez stated that Magneto would serve the mutant cause better as a martyr and then jettisoned his chambers into space. The security footage somehow has a shot of Magneto's chambers being jettisoned from a long distance with Cortez's martyr comment voiced over.
Continuity mistake: In the flashback during Magneto's memorial, when the Nazis are approaching his home it says "Lehnsherr" on the door. After they kick the door open, the writing on the door has disappeared and either a hatch or a small window has appeared on the door from nowhere.
Continuity mistake: When Fabian Cortez is scapegoating Gambit in front of the mob, he grabs him by the blue clothing that lines the body armor on his chest. When he says to Gambit "Mark my words X-Man..." the blue clothing is now the same brown color as Gambit's trenchcoat.
Continuity mistake: When Rogue is asking about Gambit's whereabouts, she along with Beast and Xavier are close to the front of the shuttle. When the shot changes, the three of them as well as one of the astronauts are suddenly further back in the shuttle (note the doorway).
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.
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.