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.
Continuity mistake: When Wolverine is first seen, the camera pans along a barbed wire fence which is almost straight, yet in another shot, all the barbed wire is broken off the fence or is hanging down from it. (00:05:45)
Continuity mistake: 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. (01:43:10)
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).
Continuity mistake: When Cyclops knocks Lady Deathstrike down with his beam at the plastic prison of Magneto and she gets back up, her eyes are blue with the contacts. However, when she flies through the air and pins Cyclops against the wall, her eyes are their natural color, brown.
Continuity mistake: When Wolverine returns home to the Xavier mansion, Rogue greets him, they talk, and when Jean arrives Rogue leaves them alone. In one shot Rogue's hair is over her left shoulder running down her chest, but in the following shot all of her hair is at the back. (00:16:15)
Continuity mistake: When Wolverine can't sleep, he hands Bobby the soda bottle and the contents are almost full, but when Bobby blows on the bottle and hands the chilled bottle back to Wolverine the contents are much lower. Then when Wolverine drinks the Dr Pepper, the bottle is full again. (00:31:00)
Continuity mistake: When we see Logan in Cerebro with Professor Xavier trying to find Nightcrawler, Xavier's metal hat in one shot is completely covering his ears, yet in several shots after it's not covering his ears and the hat is a lot looser. (00:19:30 - 00:20:30)
Continuity mistake: When Wolverine is in the schools kitchen with Iceman, you see Iceman point to a cupboard. If you watch closely between shots Iceman's finger changes from being a little limp and pointing down, to being straight and pointing up. (00:29:35)
Continuity mistake: During the mansion invasion scene, Wolverine jumps from the balcony level. He drops onto one knee, and stabs two soldiers with his claws. He then stands up and throws them off. In the shot from behind once he's thrown them he's still part crouching, but in the very next shot from the front, he's fully upright. (00:40:10)
Continuity mistake: When Wolverine is tramping through the snow to Alkali Lake, you get a long shot of him looking at a wolf with the sides of his hair are styled so they're sticking up at least three inches. After he goes through the gate, his hair is totally flat. (00:06:10 - 00:06:55)
Continuity mistake: Near the start Logan is inside Cerebro with Xavier and Xavier turns to talk to him. The chair he's sitting in doesn't go any higher than the top of his back, yet a few shots later, the chair is now above his neck. (00:20:45 - 00:21:15)
Continuity mistake: At the beginning of the film in the museum scene when we first see Pyro and Iceman, there is a man with a green sweater that is sitting behind Iceman. In the next shot he's sitting beside him, then is behind him in the next shot. You can also that in one shot he is looking in Pyro's direction but in the next shot, he isn't. (00:09:05)
Continuity mistake: In the scene where we see the X-Men and Magneto inside the jet at Alkali Lake, they are going over a map of the base, the camera cuts to Nightcrawler and Pyro, in this shot we see Pyro with his hands behind the head rest not visible, yet in the following shot his hands are now visible above his head, then the shot after back to being behind the head rest. (01:15:20)
Continuity mistake: When Mystique (as Dr. Jean Grey) tries making out with Wolverine, we see that the scars that Wolverine made in the first film are vertically across her stomach. But in X-Men, when Wolverine stabs Mystique with his claws, the marks (which later become scars) are horizontally across her stomach. (01:15:15)
Continuity mistake: This is on the DVD. When Storm and Nightcrawler rescue the children Storm shouts "Jubilee" but the subtitles have her name as being "Julie". (01:27:50)
Continuity mistake: When Magneto is reversing Cerebro, he is floating and turning clockwise. Just as he passes the door there is a cut and suddenly he is back facing Professor X as he comes back down. (01:40:00)
Continuity mistake: When the SWAT team raid Xavier's mansion, a SWAT member walks into the kitchen where Bobby is but Wolverine grabs him which causes him to fire. The napkins on the table get shot at, then fall onto Bobby who is kneeling down behind the kitchen table, but in the following shot they are falling down again. (00:35:10)
Continuity mistake: When Cyclops encounters Lady Deathstrike at Magneto's prison and knocks her down with his optic blast, watch her eyes as she's getting up from the ground. Instead of the greyish white they should be while under the control of the serum, they're a rather nice looking shade of blue. When it shows her standing, they are white/grey again. (00:34:45)