Continuity mistake: When Magneto lands the Golden Gate Bridge on the island, as it hits land it is still very light. When the Brotherhood start to walk toward the island, it cuts to a wide shot of them still walking on the bridge, and it's suddenly dark.
Continuity mistake: When Logan pulls out the two horns from his stomach, the camera shows two holes on the singlet as part as his wounds. In the following scenes, the holes of the t-shirt have recovered (I know Logan has healing ability, but not his clothes).
Continuity mistake: 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 mistake: 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.
Continuity mistake: In the scene on Alcatraz, Collosus throws Wolverine at Magneto. After Wolverine is dragged along the floor and Magneto says something to him, Wolverine looks up at Magneto from the wrong direction (this is explained when you look at the deleted scenes but doesnt fit in the final cut).
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: After Magneto declares war, troops are briefly seen exiting from a bus with brown boots. As they line up, you can see the boots have been replaced with black rubber ones.
Continuity mistake: When Magneto is moving the cars on the bridge at the end, a reddish van in the center of the road is moved to the side. A couple of shots later, the same van is again moved from the center to the side.
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.