Continuity mistake: When Magneto is showing Asteroid M to the delegates at the U.N. meeting, the Genoshan delegate he forced to sit down has either moved to another seat entirely or the people that were sitting around him moved to different seats and other people filled in their seats.
Plot hole: Some of the footage Magneto is showing the delegates at the U.N. meeting includes footage Magneto could not possibly have had access to even if such footage existed, such as the X-Men having mission briefings in the War Room, the Morlocks living in the sewers or Warren Worthington emerging from being buried under several feet of snow at his secluded home in the mountains.
00:03:10 - 00:04:05Phaneron
Continuity mistake: The exit door and stairwell outside of the town hall are shown to be at the very edge of the building when Proteus goes through it. When Xavier, Beast, Rogue and Wolverine use the same door and stairwell, the building suddenly stretches on for several more feet.
00:13:20 - 00:13:55Phaneron
Revealing mistake: When Proteus is leaving his father's home while possessing the police officer, the green glow of his eyes doesn't stay in place as he is moving. You can see the green glows leave his face and float in midair with the eye slots on the face turning black. It appears that the animators couldn't keep the glowing eyes synchronized with the body movement.
Other mistake: When the two civilians are walking past Joe McTaggert's campaign posters, they are shown to be walking unusually fast, almost as if the ground beneath them is moving them forward between strides (similar to as if you were walking on a moving sidewalk inside an airport).
Continuity mistake: At the very end of the previous episode after Proteus had messed with Wolverine's sense of reality, Wolverine is shown whimpering in an open area. When Wolverine is shown at the beginning of this episode still whimpering, he has suddenly moved next to a treeline. Given the state of shock he was in, it's doubtful he would have gotten up and moved.