Continuity mistake: Archangel's alumni status (or lack thereof) with the X-Men varies throughout the series. Later episodes showed him to be an original member of the team just like in the comics, yet when he first appeared in Season 1, none of the other original members in the show (Cyclops, Jean Grey and Professor X) seem to know who he is. The time traveling mutant Shard also states in Season 4 that he is destined to eventually join the X-Men.
Continuity mistake: The Sentinel that is intercepting Jubilee when she is running back home to check on her foster parents is initially following her along the sidewalk from behind, but suddenly catches up to her in a perpendicular path from the street. There are only two Sentinels shown in this scene and the other one caught her from the front as it turned a corner, so it couldn't have been a different one.
Continuity mistake: Immediately after Storm, Wolverine, Beast and Morph exit the Mutant Registration Center, Beast and Wolverine are shown to be running alongside Gambit and Cyclops. However, mere moments later, Gambit is shown to be blowing up a security fence so Storm, Wolverine, Beast and Morph can rendezvous with Gambit, Cyclops and Rogue.
00:06:45 - 00:07:20Phaneron
Continuity mistake: When Rogue goes to touch Wolverine with her bare hand to stop him, she is shown removing the glove from her right hand. After Wolverine collapses, Rogue is now missing the glove from her left hand, and her entire left arm, including the hand, is solid green.
Continuity mistake: At the end of the previous episode, Rogue says to Cyclops "You look nervous as a long-tailed cat in a room full of rocking chairs," to which he responds, "I just wish I knew what was happening in there." Cyclops then immediately looks to his right and sees military vehicles approaching and says "We've got trouble." At the beginning of this episode, the same scene is shown again, only this time Gambit says "If that was me in there you wouldn't have to worry" before the military vehicles are shown to be arriving.
Continuity mistake: When Sabretooth is sitting in the hover chair in the War Room, the chair is shown to be hovering up and down in the wide shot, but when a closeup of Sabretooth is shown, the background behind him remains stationary, indicating the chair is also stationary.
Continuity mistake: When Jubilee blasts Sabretooth through walls of the War Room and outside, it is shown to be on the mansion's ground level. Many other episodes however depict the War Room to be in the underground levels of the mansion, specifically in the episode "The Unstoppable Juggernaut" where the War Room is still intact after the mansion is destroyed from the ground up.
Continuity mistake: When Gambit is avoiding the electrified coils in the Danger Room, his normally black and red eyes are colored like a normal person and his gloves are entirely fingerless whereas they are usually only fingerless for the thumb, index and pinkie fingers.
Continuity mistake: Gambit and Jubilee are shown to be grouping together what appears to be several pieces of malleable rebar. When the shot changes to Gambit reassuring Jubilee that Storm is alive, he is shown to be working with a single piece of rebar. When the shot changes again, they are back to working with a bunch of rebar.