Continuity mistake: When Graydon Creed is interrogating Carly, their positions in the room are different depending on the shot. When first shown, she is tied to a chair, with a bare wall a few feet to her left. When Wolverine enters the room, he enters through a door that is now on the wall on Carly's left that was previously bare. When Wolverine tells Creed to let her go, they are suddenly right next to a wall on Carly's right. Then when Creed is pointing the gun at Wolverine and for the remainder of the scene, Carly is suddenly facing the door Wolverine came through.
00:15:35 - 00:17:50Phaneron
Continuity mistake: When Wolverine is infiltrating the Friends of Humanity's headquarters, and later when he is talking to Graydon Creed in their auditorium, some shots show him wearing a gold wristband on his left wrist, and other times he is not wearing one.
00:06:20 - 00:14:30Phaneron
Continuity mistake: When the opening of the Astral Plane is first shown emerging from Mt. Kilimanjaro's Kibo summit, the summit is correctly depicted as being somewhat flat. Near the end when the opening of the Astral Plane is diminishing, the mountain summit is shown to have a pyramidal peak.
00:02:35 - 00:16:50Phaneron
Continuity mistake: The bommerang that Xavier uses to throw at the jungle warrior astride the pterodactyl appears from nowhere. While it probably belonged to the warrior himself, neither he nor the other warrior with him were shown to have dropped it when they swooped by and captured Magneto and knocked Xavier down.
Plot hole: After Magneto and Xavier discover that their powers have vanished, Mr. Sinister is shown to be watching them through surveillance footage, zeroed in on their faces from a straight angle. At this point, Magneto and Xavier are standing at the edge of a cliff in the Savage Land, which is a jungle hidden in Antarctica. There's no conceivable way Mr. Sinister could have security footage of them from where they are located. Any camera would have to be mounted onto a tree, and the cliff is at a considerably higher elevation than the jungle itself, as well as a considerable distance away. Even if Mr. Sinister was able to zoom in on them from such a distance, the treeline being lower than the cliff would only allow him to view them from a low angle, and that's only if the cliff wall didn't obscure them.