Continuity mistake: Rogue rips off Donald Pierce's cybernetic left arm, but when he is first shown running away, his right arm is the one that is missing. When he catches up with Sebastian Shaw in the secret passageway, his left arm is back to being the one missing.
Continuity mistake: When Cyclops blasts a hole in the floor beneath Sebastian Shaw and causes him to fall through it, Shaw lands on a catering table. Later when Beast jumps down the hole to attack Shaw, Shaw is emerging from underneath heavy rubble rather than a catering table, and he is inexplicably shirtless. The rubble also changes from being brown just before Beast jumps down the hole, and is then white after he lands. Additionally, the floor goes from being black-and-white checkered to a solid brown color.
Continuity mistake: When Beast says "We appear to be at the mercy of our hosts," he is noticeably further away from Cyclops than he is from the rest of the episode. The captive X-Men are chained to the floor with not much slack, so he could not have simply moved away from Cyclops on his own.