Plot hole: After Storm's attempt to escape the Genoshan prison is thwarted, she ends up in the ocean right at the shoreline of the beach, where she is captured by a Sentinel. Aside from the fact that it makes no sense for a Sentinel to be hiding in the ocean in the event that a mutant tries to escape the prison, there is absolutely no way that a two-story tall robot could hide in the ocean right by the beach, as the water would be way too shallow. You can even see that the water level only goes up to the Sentinel's ankle area when it is standing upright in the ocean. (00:03:15)Phaneron
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.
Factual error: When Professor X is calling Moira McTaggart in Scotland, the phone number he uses is shown to have only dialed the exit code of 011, followed by a fictional seven-digit number with a 555 prefix. Since he is calling from the United States, he would have to dial the country code (44) and area code for the right part of Scotland. Plus UK numbers at that time had at least 9 numbers. (00:08:20)Phaneron
Revealing mistake: When Quicksilver is fidgeting inside his containment shell, the animators neglected to properly sync his body movement. You can see that his shoulders are not "connected" to his arms, as if his head and shoulders were separated from the rest of his body. (00:16:00)Phaneron
Other mistake: Rogue states that this is Jubilee's first Christmas as an X-Man. However, Jubilee was already a member of the X-Men when Senator Kelly declared his candidacy for President in season 1, and the season 2 premiere episode showed him being sworn-in as President. Election Day is in November and the President is sworn-in in January, so Jubilee should have already had at least one Christmas as a member of the X-Men. (00:02:00)Phaneron
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