Continuity mistake: When Angel is about to get the "cure" in the San Francisco skyscraper, you can see the reflection of San Francisco in the outside of the building - a huge hill with lots of buildings, and a large white tower at the very top. But when the camera switches to inside the building, looking outside, the view has suddenly changed to a view of the bay, and Alcatraz.
Continuity mistake: When Magneto and Charles Xavier are in Jean Grey's house (when she is older and making everything around her float in the air), watch the book shelf when it falls down. At least 25 books fall out of the top shelf and in the next few shots you see that the number of books fallen has minimized greatly. (00:45:00)