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?"

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.

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.

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

Plot hole: Since Logan's highly developed sense of smell detected Mystique as Storm in the original film (right before he impaled her), why wasn't he able to detect that she wasn't Jean Grey in the tent in the second film?

Continuity: When Wolverine locks up Stryker in the chopper, he just wraps the chain around Stryker's chest to start with. But when he completes the link and pats Stryker on the shoulder, Stryker's hands are suddenly behind his back.

Audio problem: When Bobby's brother dials 911 you hear 3 tones (for the 3 digits he dials). But the 3 tones aren't the right tones you hear when you dial 911 from a touch tone phone. In fact the 2nd and 3rd tones should be the same because it's the same digit but they were different. As if someone just dialed 3 random digits. And there's no doubt he dialed 911 because the operator answers "911".

Deliberate "mistake": Almost trivia, but not quite. When Mystique's looking through the guard files to find a suitable candidate, lots of photos flash up very quickly before she finds the guy she uses. Of note is that Bryan Singer pops up in guard uniform (with his own name), and so does someone called "Donner, L". This is most likely referring to Lauren Shuler Donner, one of the producers, and sex is specified as "F", but the photo is of a stubble-coated man.

Continuity: When the SWAT team are inside the mansion, Logan jumps down to save Rogue Bobby and John, and he chucks two guys back some distance. In the overhead shot, the four SWAT guys are together on the floor, instead of two of them being some distance away like we saw in the previous shot.

Continuity: When Wolverine, Rogue, Bobby and John are in Bobby's house and are talking to his parents, his dad says to Wolverine "What are you a professor of?" Just after this the camera cuts to an overhead shot, there is an orange pillow at Bobby's brother's side, but in all following shots the orange pillow has vanished and is replaced by two striped pillows.

Continuity: When Bobby gives Rogue the clothes, it's shown that she is not wearing a bra. But when she is draining John's power later, a bra strap is visible on her shoulder.

Other: When the X-Mansion is being attacked, Wolverine jumps off the stairs onto two soldiers and throws them backwards with his claws. The soldiers are level with his wrists as they begin flying back. If they had been thrown in such a way, they would have followed the same path through the air as Wolverine's claws.

Continuity: When Wolverine is fighting Deathstrike, Wolverine lands on a steel-like platform hanging over the water tank. When Deathstrike gets underneath and starts stabbing Wolverine, she is on his left side, yet when the camera cuts to a view from underwater looking up, she is on his right side.

Continuity: When we see Logan enter the mansion and Rogue comes to greet him, Iceman is standing just behind Rogue, then the camera cuts to a front view, and Iceman is now shoulder to shoulder with Rogue, then it cuts to the back again, and he is back behind Rogue.

Revealing: Towards the end, when the mutant children are running through the snow, Artie (the green-tongue boy) isn't really bare-foot, he's wearing coverings that protect his feet from the snow.

Continuity: When they show a shot of the captured children in the cell, all of the children are barefooted, but when they show the children running in the snow after escaping the dam, a few of them are wearing brown slippers. When did they get a chance to put those on?