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. (02:01:40)
Trivia: During the scene in the bar with Mystique and the prison guard, the person on the TV is Dr. Hank McCoy - this is the real name of X-Man The Beast.
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. (00:36:40)
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. (01:27:50)
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. (00:23:10)
Continuity mistake: 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. (00:15:45)
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. (00:53:55)
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. (00:09:35)
Continuity mistake: In the beginning when we see Nightcrawler get past the metal detectors, in the first shot we see him standing still next to a striped bench. The following overhead shot, the bench is now completely red with no stripes. (00:02:35)
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. (00:23:10)
Continuity mistake: When Wolverine handed the bottle of Dr Pepper to Bobby, he was holding the body of the bottle. But when the shot changes to show Bobby taking the bottle, Wolverine was holding the bottle neck. (00:30:00)
Continuity mistake: In the scene where Wolverine is talking to Stryker in the mansion corridor, Bobby creates an ice wall between them, including the wall. Shortly afterwards when they leave and Bobby takes his hand away, the wall suddenly has no frost on it at all. (00:41:45)
Trivia: Bryan Singer is the guard who initially rolls Xavier into the guard room in the glass wheelchair before passing him off to the other guards. (00:29:10)
Trivia: In the scene where Mystique is going through the files on Lady Deathstrike's computer to find the guard's profiles, one of the guards is director Bryan Singer (he's listed as "Singer, B"). (00:23:45)
Continuity mistake: When Nightcrawler is inside the Oval Office, he jumps on the President, and the President's leather chair changes direction between shots. (00:04:35)
Continuity mistake: When Xavier is in the plastic prison with Magneto, at the end of this scene, you see Xavier put his hands on the doors of the prison, but in the following shot from outside the prison his hands have changed positions on the doors. (00:33:10)
Suggested correction: When Xavier is in the plastic prison with magneto, at the end of the scene Xavier has not changed his hands positioning, his right arm is up and his left arm is half way, on the following shot outside the prison his right arm is up and his left arm is up half way, it's a mirror image.
The mistake isn't saying his right and left hand have switched because they were confused about the "mirror" image. You can see the left arm is lower. At first the left elbow is above the frosted part, but in the next shot, it's well below and the hand is closer to the frosted part.
Revealing mistake: In the beginning of the movie when Wolverine puts the cigar out in his hand, you can see the mark of a wedding ring on his ring finger (Hugh Jackman is married). Even if Wolverine got married during the "blurred" bit of his memory so doesn't remember it (tenuous at best), his healing ability would have removed any ring mark. Either way it just doesn't belong. (00:19:50)
Continuity mistake: In the scene where Stryker is walking through the tunnel in Alkali Lake, a drop of water drips onto his glasses thereby alerting him to the breaking of the dam. He examines the drop on his lens, but when he puts his glasses back on, the lens is dry. (01:29:05)
Continuity mistake: When Jean and Storm first meet Nightcrawler and hold him upside-down in mid-air, his cloak hangs down ("up" by his viewpoint) in the shots facing him, but in the shots facing Jean and Storm his cloak is not hanging down (so we can see the two of them).