Continuity mistake: When Rogue is seen for the first time, her hand is moving up photographs on the wall, and if you look closely there are some kind of red poppies when she reaches the end, yet when it cuts to another shot a bit further away, her finger is a lot further down the wall from the red poppy/flower. (00:04:15)
Continuity mistake: When Cyclops and Storm are in the train station, Storm is held up by Sabretooth, Cyclops spots this and starts to walk over to help. He stretches his arms out between a lot of people to push two people out the way, yet when the shot changes to Toad's POV all the people around him are at least two to three feet away from him. (00:50:30)
Continuity mistake: Just after the soldier hits the young Magneto with his gun, the guy on the left is holding him and he turns away looking at the ground (probably so he knows where to fall). Yet in the following shot, the boy is looking up on top of the guy who is facing up. (00:03:35)
Revealing mistake: During the montage that introduces Xavier's School about 27 minutes into the film, you briefly see Cyclops shooting several Frisbees/clay-pigeons out of the air. Watch closely, and you will see that the falling debris from all of the clay-pigeons simply "fades away" shortly after each one explodes. They aren't burning up or disintegrating from his beam. You can see them "fade away" as the animation finishes when each one explodes. A shortcut in the CGI rendering.
Revealing mistake: The "copper" straps used to restrain the heroes in the Statue of Liberty are actually made of foam or some other malleable material. They flex considerably as the characters struggle. (01:18:28)
Continuity mistake: When Wolverine has just walked into Xavier's office for the first time, a girl picks up her book then runs towards Wolverine. Her left hand is on her bag, but in the following shot when Wolverine looks over his shoulder, her left hand is now on the left strap of the bag. (00:24:10)
Continuity mistake: When Wolverine and Rogue are in Wolverines truck, just prior to the crash, we see them driving near huge trees with thick leaves that can't be seen through. When Rogue says the line "You really should wear your seatbelt", the view out her window shows a handful of trees that one can see through for a mile.
Continuity mistake: When Senator Kelly meets Magneto for the first time, it's outside and cold. When you see Kelly his breath shows blowing to the left of the screen. But when you get the reverse angle of Magneto and Mystique their breath also goes off to the left of the screen. It should be blowing to the right.