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. (00:18:30)Phaneron
Continuity mistake: Wolverine first enters the sewers by ripping away a fence in the subway. When Jubilee and Gambit follow him, the fence is still intact. When they get closer it is torn again. Odd, really, because on the whole this show has few continuity errors, like self-mending clothes in other cartoons.
Continuity mistake: Magneto straps Wolverine to the port side of a boat and then drops the boat on a warehouse. When Gambit is freeing Wolverine, Wolverine is suddenly on the starboard side of the boat. After Gambit frees Wolverine, they are both shown to be on the boat's port side. (00:17:00 - 00:18:00)Phaneron
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. (00:15:55 - 00:17:05)
Continuity mistake: Beast disarms a member of the Friends of Humanity whilst perched on a street lamp. When the angle changes to a wide shot, Beast is much higher on the lamp post and would have been too far out of reach to disarm the man in the first place. (00:11:45)Phaneron
Continuity mistake: The exploding playing card that Gambit uses to destroy a few Sentinels and draw the rest above ground is cleverly shown to be the ace of spades (also known as the death card in some folklore), but the card he is shown charging up before the Sentinels see it is the 2 of diamonds. (00:12:10)Phaneron
Continuity mistake: When Gyrich is in the car trying to get Trask on the phone, he is shown to be sitting in the backseat on the passenger side (note the windows immediately to his right and behind him). When his driver crashes the car into a tree, Gyrich is shown exiting the car from the front passenger seat. (00:08:00)Phaneron
Continuity mistake: When Graydon Creed is interrogating Carly, their positions in the room are different depending on the shot. When first shown, she is tied to a chair, with a bare wall a few feet to her left. When Wolverine enters the room, he enters through a door that is now on the wall on Carly's left that was previously bare. When Wolverine tells Creed to let her go, they are suddenly right next to a wall on Carly's right. Then when Creed is pointing the gun at Wolverine and for the remainder of the scene, Carly is suddenly facing the door Wolverine came through. (00:15:35 - 00:17:50)Phaneron