Minor Plot hole: Mystique, disguised as Bobby, challenges Rogue in the school's court and tells her that everyone is furious at her and that she should leave for good. And she does exactly as told – but they didn't tell her where to go or how to get there. She went to a train station and Magneto happened to know which train to cut in half. Pretty lucky guess there Magneto!
Minor Plot hole: But let's go a little deeper. How could Rogue get on that expensive looking train ride? She was supposed to be completely broke. She hitched rides with strangers to Canada, only drank water and was salivating at the sight of money – not sure whether she wanted to eat it or spend it on food. Then she was brought to Professor Xavier's school and got enrolled for free. How did she pay her ticket?
Minor Plot hole: Oh we're not done baby; we gotta go deeper. Why couldn't Mystique simply impersonate Bobby and pretend to bring her on a sexual adventure in the woods to show her his permafrost cock and simply kidnap her right there? There really wasn't any need for the bad guys to push her to leave the school and hope they would fall on her by accident while they could have simply taken her right away. Why put luck as your middle man?
Minor Plot hole: I'm going all-out in the depths of deepness - I'll pull out I promise. The X-men know Mystique exists: she is the right-hand woman of Magneto. But they seem to have absolutely no counter-measures against her potentially deadly infiltration attempts. In fact, she manages to get in the school without being noticed by anyone and inject some black diarrhea in Cerebro. Was Charles Xavier simply hoping that Mystique would never show-up to his school? Because she could totally have been there every other week to spy on their operations.
Major Plot hole: Magneto has a Lego mask that cockblocks Xavier from screwing with his is mind and knowing his location. If only Magneto was always surrounded by three other mutants like, let's say: Toad, Sabertooth and Mystique – perhaps he could have used Cerebro to find exactly where Magneto brought the recently kidnapped Rogue. And another thing, if Magneto's mask is so awesome and the best counter to Xavier who is pretty much the strongest opponent they are facing – why didn't he make a few other helmets for his henchmen? Not only would it protect them from potential mind rapes – but it would also make sure Xavier would never be able to spot them with his giant machine.
Plot contrivance: Bar owner puts his gun to Wolverine's head instead of keeping a safe distance after he just witnessed a 6 feet tall man push metal blades out of his fist. I'm pretty sure the first rule of gun vs knife fight is for the gunner to actually stay at range....you know, because it's a ranged-weapon.
Plot contrivance: Magneto shoots a gun to a police officer's head and maintains the bullet in place with his powers. Pretty cool. But why is the police officer staying there while a bullet is painfully rotating on his frontal bone? He could have consciously taken a step-back or unconsciously as a reflex to a painful stimulation.
Plot contrivance: There is a giant UN dinner in front of the Statue of Liberty – guards are everywhere. Not just the incapacitated ones on the island but the hundreds of others around the banquet. And yet no one notices a giant metal module being lifted in the air and being attached to the Statue's torch.