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.
Audio problem: When Wolverine says to Sabretooth "You taught me that you can't count on your friends," Sabretooth is the actually the one mouthing the last three words. And when Sabretooth says "I saved both our lives you..." Wolverine is the one mouthing the entire line.
Continuity mistake: When Rogue is attempting to rescue Gambit from the avalanche, Gambit's right hand goes from being gloveless to gloved. There is even a point when she is pulling him out of the snow that a glove instantaneously materializes on his hand and then disappears just as quickly.