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
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.
Continuity mistake: During Xavier's flashback, Jean Grey goes from wearing her current (as of the show's broadcast) uniform while training in the Danger Room to her original "Marvel Girl" uniform when Amelia is leaving the mansion. Additionally, when Xavier is talking to Amelia in the Danger Room's control room, he is in his usual hoverchair, yet when Amelia is leaving the mansion, he is in a regular wheelchair.
Continuity mistake: When Bishop and Shard first appear in the alternate present timeline, they appear right next to the doorway of the infirmary where Wolverine, Storm and others are taking refuge. When the shot changes to Bishop stating that they have arrived too late, he and Shard are suddenly several yards away from the doorway.