Corrected entry: When in the Statue of Liberty, Magneto magnetizes the bars to keep Wolverines hands pointed at himself and hang him against the wall. Wolverine decides to stab himself, which makes him fall. Maybe I'm wrong, but why would stabbing himself make the magnetism wear off so he can fall?
Corrected entry: It is established that the X-Men's base of operation including Cerebro are in underground levels. In this scene, you see Bobby walking with two friends talking about Rogue missing. Mystique (as Bobby also) walks out of the round elevator as the real Bobby walks past. They are on the main ground floor. The next shot, Mystique as Bobby is in the underground level standing in front of the door to Cerebro. Why is she in the elevator in the first place that she'd exit on the ground level, and why would she exit at the ground level if she just has to go back in to go down to the basement to access Cerebro?
Corrected entry: Near the end, Cyclops tells Storm to "fry" Magneto. Magneto then answers, "..lightning bolt in a small copper space..." meaning that everyone would be "fried". This is total baloney, as the bolt would hit Magneto directly, then discharge into the floor of the statue and dissipate in energy through the whole statue. Magneto would receive a direct hit and as the main conductor and would be instantly killed. The others would also be shocked, but to a substantially lesser degree and certainly not life-threatening. However, Magneto seems to either not know this, or more likely is lying with the (correct) assumption that the others don't know that either.
Corrected entry: Xavier might not want to kill Magneto outside the train station, but he could easily have used Sabertooth to knock his protective helmet off or slam him into a wall and knock him unconscious. If he had done this immediately (before Magneto pointed everyone's guns back at them, after which it was obviously too risky) he could have captured Magneto then and there. Granted, not very good for the film, but it still should have occurred to him.