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: When Leech is telling Lady Deathstrike that Callisto forced him to steal from her, she has her hand wrapped around his neck. When the shot changes, her hand is now gripping him by the chin. (00:03:00)
Continuity mistake: When Leech picks up the gun to try to defend himself from the Reavers, he is in an underground area with brick walls. When Lady Deathstrike grabs him and asks why she should spare him, they are now standing in a tunnel with walls similar to a cavern. (00:02:50)
Continuity mistake: When Wolverine regains consciousness, he runs away and turns around, and there is a tunnel system directly behind him, and the alien craft on his right, almost within arm's reach. A few shots later, the alien craft has disappeared. When the shot changes again, the alien craft has reappeared. (00:17:45)
Continuity mistake: When Wolverine brings his jeep to a screeching halt, the windshield either changes color or appears out of thin air. (00:07:34)
Continuity mistake: When Gambit presses the button to receive Leech's call, the antenna is on the left side of the phone. When the shot changes, the antenna is now on the right side. (00:05:42)
Continuity mistake: When Wolverine is trying to get to Professor Oyama, he slashes twice at the door leaving six claw marks. When the door is shown again after Wolverine is reacting to the explosion, there are suddenly several more claw marks without him ever slashing at the door again. (00:11:40)
Continuity mistake: The three tear marks in Wolverine's uniform from when Lady Deathstrike slashes him change position several times. When she first slashes him, the tear marks appear on his chest. Other shots show the tears to be closer to his abdomen. (00:13:50 - 00:16:00)
Continuity mistake: When Professor Oyama says "Adjust the feed accordingly," you can see in the reflection of Wolverine in his glasses that the device that has been on Wolverine's left leg throughout the scene is missing. (00:10:20)
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: 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: The scratch marks Lady Deathstrike makes in the alien ship don't appear until she mentions them. (00:04:00 - 00:05:15)