Minor Plot hole: The VERY important character of Angel is introduced in a strip club. She is in an open-room with dozen of extras right behind her and decides to show her insect-wings to Charles and Erik right after it has been established that mutants keep their powers as secret as possible. The quick flapping wing noise didn't help either. Wtf was that?
Minor Plot hole: Emma Frost has many great powers. Some of them include the ability to change her body into diamond and super-human strength. This strength is showed early on in the film when she tosses Erik out of Shaw's boat with a single arm swing. BUT later, both Erik and Charles are able to pin her to the ground (PG-13-wise) without any real effort. Where did her super-strength go ? And what about her staying in prison for no reason ? She showed the ability to escape ? Was she bored or something ?
Minor Plot hole: Even if young Magneto could not kill Sebastian Shaw, it is surprising to see that when the latter kills his mother, Magneto sees fit to kill all the guards around him and destroy the entire room......but not a single tiny attempt of violence towards his mother's killer.
Major Plot hole: At the end of the film, when Charles and Erik divide the mutants into two separate groups with different objectives for the future, the second team decides to teleport out of enemy territory to a safer place.....without the first team. This is interesting considering the fact that Charles and Erik were still friends and one of them was lying on the ground with a bullet wound in his spine. Did they expect him to stand up, do a back-flip for good luck and swim back home ?
What if the military launched other missiles at them ? Both mutants with the powers to save everyone, Magneto and Azazel, would not be around to save them. So basically, Erik left the group there alone to at best make it home with much trouble, or at worst explode by another volley of missiles.
Plot contrivance: Sebastian Shaw, the villain of the movie and overall badass, makes his climactic final entrance by opening an automatic door in the sub when Magneto is looking away. However, the sub was moved out of the sea into the sky, thrown on the shore and barrel-rolled a few times. How was this automatic-door still operational?
Plot contrivance: Of all the places in the World, a young Mystique tries to rob a rich family....and meets Charles Xavier in the kitchen. What are the odds right?