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.
The Unstoppable Juggernaut - S1-E8
Continuity mistake: When Storm, Rogue and Jubilee are out driving and looking for Wolverine, Rogue's headband is the same color as her flesh. (00:04:45)
The Unstoppable Juggernaut - S1-E8
Continuity mistake: When the team arrives at the destroyed mansion at the end of the previous episode, Cyclops' seat is blue, Rogue says "It can't be" while raising her right hand up to her mouth in disbelief, and Wolverine is growling and extending his claws. When the team is shown arriving at the destroyed mansion at the beginning of this episode, Cyclops' seat is now light-red, Rogue says "It can't be" while her arms remain at her sides, and a silent Wolverine is casually putting on his mask and walking towards the exit ramp of the Blackbird. (00:02:23)
Slave Island - S1-E7
Continuity mistake: When Cameron Hodge is telling Gyrich and Trask about Cable, the books on the table move closer to Hodge between shots. (00:13:10)
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. (00:02:15)
Continuity mistake: When Storm is having a flashback to her childhood in a fit of claustrophobia, she is depicted as a Caucasian girl with red hair. (00:03:35)
Continuity mistake: When Sabretooth tells Jubilee that her powers are useless if she can't use her hands, the glove on her left hand turns from yellow to brown multiple times. (00:15:50)
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. (00:04:35)
Continuity mistake: When Wolverine says to Sabretooth "Be careful what you ask for," his arms are yellow. (00:17:05)
Continuity mistake: The stains from the tomatoes that are thrown at Beast disappear from his jumpsuit. (00:10:05 - 00:10:55)
Night of the Sentinels: Part 2 - S1-E2
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. (00:11:55)
Night of the Sentinels: Part 2 - S1-E2
Continuity mistake: When Rogue catches the security guard from the collapsing tower, he has black hair. When she is flying through the air with him as well as when she dumps him in the grass, his hair is red-orange. (00:06:50)
Night of the Sentinels: Part 2 - S1-E2
Continuity mistake: When Wolverine is playing pool, he scratches the cue ball and the cue ball is then back on the table without him retrieving it. (00:13:35)
Night of the Sentinels: Part 2 - S1-E2
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 - 00:07:20)
Night of the Sentinels: Part 2 - S1-E2
Continuity mistake: After Cyclops tells Gambit to blow up the fence and Rogue flies into frame, her headband and the patches on her uniform that are all normally black are now red. Additionally, the black encircled X on a red background on the left side of her chest is now a yellow X on a red background. (00:06:35)
Night of the Sentinels: Part 2 - S1-E2
Continuity mistake: When Gambit says "You wanna play with Gambit? Here, take a card!" the glove on his right hand is missing, then is suddenly back on his hand when he says "House wins." (00:05:50)
Night of the Sentinels: Part 1 - S1-E1
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. (00:14:40)
Night of the Sentinels: Part 2 - S1-E2
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.
Night of the Sentinels: Part 1 - S1-E1
Continuity mistake: The position of the police cars around Sabretooth change from shot to shot. (00:01:15)
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.