Wolverine: It's time for us to move on.
Cyclops: Not everybody heals as fast as you, Logan.
It is revealed in the commentary that the man in the vegetative state that Moira McTaggert takes care of is actually meant to be the twin brother of Charles Xavier, Patrick. In the comics, Xavier has a twin sister, but this change was made to make things more interesting. See more...
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For this movie, Juggernaut is a mutant like everyone else - it's irrelevant how he got his powers in the comics. And no-one cares that there's an insect on Wolverine's shoulder!!
Factual error: Take a look at Google Earth - the section of the Golden Gate Bridge Magneto breaks off (tower to tower, with a bit of overhang, 0.9 miles at most, more like 0.85) is not long enough to reach Alcatraz - the two closest points are 0.96 miles apart, and that's the very end of a pier, which most likely couldn't support the weight of the bridge anyway.
Continuity: In the scene where Angel is about to be given the cure, there is a change in the hypodermic syringe used to administer the drug. As the camera shot switches between views of Angel being strapped in and Dr. Rao preparing the injection, the first view shows the hypodermic needle cover already having been removed. The camera switches to Angel then back. Dr. Rao, having completed the preparation for the injection, proceeds to remove the cover which had already been removed in the first shot.
Continuity: When Wolverine approaches Xavier's grave, the shadow of his head falls onto the grave. Then, after Jean has stopped telepathically speaking to him, the shadow of his head is left of the grave, even though Wolverine is in the same position. There was not enough time for his shadow to have moved that much.
Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.
Continuity: 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: 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.