- Incorrectly regarded as goofs: Various differences from the comic books. These are, by policy, not considered errors.
- Continuity: When Logan is drinking his Doctor Pepper while talking to Iceman, his grip on the bottleneck alternates between shots.
- Continuity: Wolverine takes the soda from the cabinet and pops the top off. Before taking a drink, he hands it to Bobby (Iceman) to cool it off for him. In the next shot of Iceman, Wolverine's arm, and the soda bottle, the amount of soda has noticeably decreased. In the third shot, we see Wolverine and the now icy bottle with the soda level returned to the same level as the first shot.
- Continuity: When the X-men jet is trying to dodge the rockets, there are a few close-ups of Bobby showing that the seat in front of him is empty. In other shots before and after the close-ups of Bobby, it shows that Rogue is sitting in that "empty" seat.
- Continuity: While the X-Men are running away from the lab, Jean's limp disappears during one shot.
- Continuity: During the "crash landing" of the plane, Rogue's seatbelt changes position between shots.
- Continuity: During the attack on the school, one of the soldiers opens fire in the kitchen and the Dr Pepper bottle on the counter changes places between shots.
- Revealing mistakes: Nightcrawler is visible in the shadows behind the children before he and Storm arrive at the cell.
- Crew or equipment visible: Towards the end of the scene where the mansion is invaded by Stryker, Bobby, Rogue, Pyro and Wolverine are running to the secret passage. As they run down a corridor, a camera is clearly visible moving into the roof of the set.
- Continuity: As water begins to leak into the underground tunnel, Stryker removes his glasses and a close-up shows several drops falling onto one lens. When he replaces his glasses, both lenses are dry.
- Plot holes: Since Senator Kelly died in the middle of the first movie, his subsequent appearances have been impersonations by Mystique. But any U.S. Senator's personal and political obligations fill up nearly every waking hour. Given that there is only one Mystique, and that she impersonates several other characters in addition to appearing as herself, "Senator Kelly" frequently disappears for hours or days at a time. In the real world or even the comic book world, her intermittent use of Kelly's likeness would be quickly uncovered as bogus by his family or staff.
- Audio/visual unsynchronized: When Magneto is changing the metal plates in the underground Cerebro with his magnetic powers, he ascends with a cape on his back. Yet, when he descends, he's not wearing the cape any longer.
- Continuity: In the scene in the lab where Nightcrawler is going to save the kids in the cage below, you see him in the shadows of the cell in an inside close-up, but in the next shot, he is on top of the bars. Then, when he is about to teleport into the cell, you can see him again in the close-up of the cell shadows, then emerging from the same shadows.
- Plot holes: When Stryker visits Magneto to interrogate him, he enters Magneto's cell while still wearing his glasses, which have metal legs. The scanning process should have caught that on his way in; if it hadn't, Magneto should be able to manipulate them and use them to escape. It was shown in the first movie that Magneto can manipulate even non-ferrous metals, so he should have been able to affect Stryker's glasses.
- Continuity: In the beginning Wolverine's hair and beard change between shots.
- Continuity: On the X Plane before the missiles hit it, Rogue scrambled to get her seat belt buckled. However, after the first plane flip, she's sitting with a smile on her face, hands in her lap, no worries. Then she's shown again gasping and holding the belt buckles with both her hands.
- Continuity: In the scene where the X-Men are in the President's office at the end of the film, they hand him a blue folder. When they have left and time begins moving again, there is a green folder and random papers on his desk. The next time we see his desk there is only a blue folder neatly placed in front of him.
- Incorrectly regarded as goofs: In the original X-Men, Wolverine is able to spot Mystique twice by catching her scent. Once when she disguised herself as a small Statue of Liberty, and another time as Storm. Yet, he does not catch Mystique by scent when she masquerades as Jean Grey and tries to seduce him. Clearly his own feelings for Jean and this sudden arousal threw him off and kept him from sensing the impersonation.
- Revealing mistakes: When Wolverine extinguishes his cigar on his hand, the end of the cigar that he pulls away from his hand is the end that was not lit.
- Continuity: In the scene where Wolverine takes the cigar and burns his hand with it, you can see a cut on his finger. But because he can heal all of his wounds he shouldn't have that cut.
- * The original poster is incorrect and this is not how sex linked characteristics are passed on.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Revealing mistakes: SPOILER: When all the X-Men and Xavier are talking with the president, supposedly everyone who is not an X-Man is frozen or time has stood still but in one shot you can clearly see someone blink a couple of times.
- Factual errors: SPOILER: After Jean Gray sacrifices herself, there is a shot of the dam showing the breach and flooded area. While the entire foreground is flooded the water level is only a few feet below the top of the dam.
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