Continuity mistake: When Professor Oyama is telling Dr. Cornelius to begin the adamantium feed, Wolverine is reflected incorrectly in Oyama's glasses (note the device on Wolverine's left leg). (00:09:50)
Continuity mistake: The warning sign on the containment vessel inside the alien ship disappears in the wide shot. (00:14:40)
Continuity mistake: When Gambit and Jubilee are chasing after Wolverine, Gambit's gloves, pants and headgear alternate between being blue, black or a combination thereof depending on the shot. (00:07:55)
Continuity mistake: When Gambit scoffs at Jubilee's notion that the X-Men are a family, his irises which are normally red are now white. (00:07:25)
Continuity mistake: When Gambit is warning Wolverine that Leech's message could be a trap, the backboard of the basketball hoop is visible over his left shoulder. When the shot changes to Jubilee offering to help Wolverine, the backboard is visibly larger. (00:06:55)
Continuity mistake: Gambit's black cowl is suddenly blue when Jean Grey is explaining that the alien spacecraft is a prison ship. (00:15:25)
Continuity mistake: The scratch marks Lady Deathstrike makes in the alien ship don't appear until she mentions them. (00:04:00 - 00:05:15)
Continuity mistake: When Wolverine says "Come on kid" to the unconscious Jubilee, the fingers of his left hand are flesh colored when they should be colored blue from wearing gloves. (00:04:50)