Continuity mistake: When Wolverine first meets Gambit, he has a slight mustache and beard. Out in the alley, after his fight with Wolverine, his facial hair is much shorter.
Continuity mistake: Gambit pushes Logan, who smashes through a wall. This hole becomes much, much smaller when Gambit climbs out into the alley. (01:10:00)
Continuity mistake: When Team X is in the African village trying to find the adamantium source, Victor is about to kill a man and Logan stops him. In the first shot, Logan says " Don't even think about it " and Victor's thumb claw on the hand Logan is holding back is very different than in the rest of the movie, as it appears to be coming out of the very tip. As the shot switches between Logan and Victor for the rest of the conversation, his thumb claw looks the same as in the rest of the movie. (00:16:10)
Continuity mistake: When Kayla 'dies', Logan leaves her body in the woods, not bothering to have a funeral or even bury her. He takes off running to the bar and it's nighttime when he arrives.
Revealing mistake: When Wolverine and Gambit are fighting, at one point Wolverine starts slicing apart a fire escape stairway Gambit is on, causing it to slowly collapse downwards. But if you pay attention, the scene is completely ridiculous. The fire-escape slowly collapses, in defiance of physics, at just the right speed for Wolverine to be able to slice it apart piece by piece (when in reality it should have fallen down all at once and then just fallen over), the pieces that Wolverine slices seem to just explode into nothingness when there should be pieces of metal building up around him, and even beyond that... The effect itself also looks very unrealistic. Poorly put together effects sequence that doesn't make any sense if you pay attention.
Continuity mistake: When the boy runs out the house at the beginning he is barefoot - we see this in a close up. When he runs off with his brother into the woods they are both wearing wellington boots.
Continuity mistake: When Logan uses his blades to take out the Humvee during the escape scene, he slashes down the entire left side cutting both tires and the body panels. However when its flying through the air, you can see the body panels are intact.
Revealing mistake: In the final scene, after Wolverine is shot in the back he turns to William Stryker. When Wolverine jumps over the debris you can see the harness. (01:35:05)
Continuity mistake: When Logan takes out the helicopter carrying Zero, as it crashes and rolls you can see a pair of legs coming out of the window. As the helicopter rolls, the body almost entirely comes out, though when Logan gets up close, the pilot is slumped in his seat, with his limbs protruding only slightly from the wreckage. (00:52:15)
Continuity mistake: In the scene where Kayle shows Wolverine she is alive, she does not have lipstick, but the last two times they show her face in that scene, she does.
Revealing mistake: When the mutants all run to Xavier and the helicopter towards the end of the film, it's blatantly obvious the actors were filmed running on a green-screen and then comped into the scene. The lighting on the actors doesn't really match the background, and somewhat more noticeably, they also don't cast any shadows on the ground.
Continuity mistake: At the end of this movie Wolverine is shot in the head, making a hole in his adamantium skull. However in X-Men we saw an X-ray of his skull, and there was no hole in it. Logan's skull and brain would've healed from the adamantium bullet fired by Striker, but the bullet hole in the adamantium forehead plating should have been visible in the X-ray image.
Other mistake: When Wolverine and John Wraith arrive in New Orleans, the street is jammed with people and the casino they find Gambit in is also completely full of patrons. Yet somehow Wolverine being thrown through a wall, his loud shouting, his slicing a fire-ladder to pieces and Gambits massive shock thrust somehow draws absolutely no attention from anyone except the main characters.
Chosen answer: Her power works by manipulating parts of the mind. Since Victor and Logan both regenerate her power can't affect them because they essentially "heal/regenerate" the part she is manipulating. Granted Prof. X threatens Logan with this in the original movies, but he is much more powerful, or could have been bluffing.