Continuity mistake: 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 mistake: 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.
Revealing mistake: 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: 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 mistake: 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 a solid orange pillow at Bobby's brother's side, but in all following shots the solid orange pillow has vanished and is replaced by two striped pillows.
Continuity mistake: 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.
Continuity mistake: Near the start in the museum, when Pyro is asked for his lighter and refuses, watch him playing with his lighter. One shot shows the top flipped open away from him, but when the angle changes it's facing towards him. There's no time it's out of shot for it to move.
Other mistake: In the scene where the mutants are confronted by the police on Bobby's front porch, there is a male officer to their right and a female officer to their left. If you watch, you will notice they are aiming their guns directly at each other.
Revealing mistake: 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 mistake: 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?
Continuity mistake: 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 mistake: When Mystique is looking around in Stryker's computer, she notices a folder marked "Cerebro", next to the "Delete" icon on the screen. However, when she opens the folder, we cut to a wide shot and the icons around the delete icon have renamed themselves, plus the cerebro folder itself has disappeared.
Continuity mistake: 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.