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)
Revealing mistake: When the old couple who give Wolverine clothes are first driving towards their house, there is an aerial shot of them driving over a bridge. This is supposed to be set in Canada (drive on the right) but it was filmed in New Zealand (drive on the left). They are driving on the right but the arrow on the road is on the left side.
Revealing mistake: When Logan is at the old couples' house and checking out his new claws in the bathroom, watch where they come out of his hand carefully - the animation of his CG claws doesn't totally replicate the movement of his hands, making it look as though they are floating around his knuckles.
Revealing mistake: When the team of Mutants are in the small village in Africa, it all goes kinda crazy and there is a bolt of lightning. If you look at the back left corner, you can see one of the flashes from a light they use to create the lightning flash.
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.
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.
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.