Continuity: In the end, when the President is visited by the X-Men, he receives a blue binder, which is laid in front of him on the table. When they have left, you see a shot including the President's desk, and you can see that the only thing he has on the table are some sheets of paper, stapled in the upper left corner, opened up. Then the shot changes to a close-up of the President, and then back again, and you see the blue binder in front of him, closed, and the papers have disappeared.

Continuity: When Magneto kills the soldiers outside Cerebro 2 their bodies are left all over the place. But when Nightcrawler, Storm and the rest of the X-men come to the same place the bodies have disappeared.

Continuity: When Wolverine attacks the SWAT member in the Mutant Academy kitchen while Iceman takes cover, there's a spot the difference competition between the start and end of the gunfight. After a second or two there are bullet holes in the back wall, the Dr. Pepper's been knocked over, the basket's gone from the corner of the table, and the chair at the right is maybe a foot from the corner. When we cut back, the bullet holes in the wall have changed position, the Dr. Pepper's righted itself, the basket's back on the corner, and the chair's now much closer to the edge. All this while Iceman's hiding and Wolverine and the gunman are fighting each other.

Plot hole: When the Drakes (Bobby's family) arrive home they are acting quite naturally, until they find Wolverine there and get a start. Later on we see that they had parked their van in the driveway right behind Cyclops' car, which Logan and company had borrowed and parked there. Wouldn't they, seeing a strange car in their driveway, be suspicious or at least enter their house asking "Bobby, are you home?"

Continuity: The mutant assistant that Stryker is controlling has the same healing abilities as Wolverine, but somehow she doesn't heal when the mind control substance is put on her neck. Even if she would still be affected by the mind control stuff, the wound she got from it should have healed.

Continuity: In the scene where the President is about to address the nation, he is handed a glass of water, but in the following shots there is no glass to be seen.

Revealing: In the scene where Storm and Nightcrawler rush to rescue the children from the holding cell, you see a shot of the cell where the children stand up and say "Listen..." before Nightcrawler teleports inside. If you look carefully, you will see Nightcrawler's silhouette in the shadow against the wall.

Deliberate "mistake": Where did Storm's accent go? The accent she had in X-Men 1 is completely gone in X-Men 2.