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.
Other mistake: Shard shows Storm and Wolverine surveillance footage of Trevor Fitzroy's deal with Master Mold, stating it was all they could get of their plan before the camera was discovered. However, the footage shows multiple camera angles that a lone mounted surveillance camera could not achieve.
00:11:30 - 00:12:35Phaneron
Character mistake: When the civilians are fleeing the coffee shop, there are two spelling errors on the coffee shop's marquee. Firstly, the name of the coffee shop is Rip Van Winkle, but on the marquee, Winkle is spelled as "Winkile." To the right of that, Coffee House is spelled as "Coffe House."