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.
The Dark Phoenix (2): The Inner Circle - S3-E12
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)
The Dark Phoenix (2): The Inner Circle - S3-E12
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)
Weapon X, Lies, and Video Tape - S3-E19
Continuity mistake: The helmet Wolverine picks up changes from gray to gold and then back to gray when he drops it. (00:05:25)
Continuity mistake: Gambit moves further away from Rogue when they are sitting on the couch. (00:03:00)
Continuity mistake: The tray of food Beast brings for Iceman has suddenly disappeared when he asks him about Lorna. (00:09:20)
The Dark Phoenix (3): The Dark Phoenix - S3-E13
Continuity mistake: When the Shi'ar beam down in front of the X-Men, Lilandra and Gladiator have a gap of a few feet between them. When the shot changes, they are suddenly standing closer together. (00:19:14)
The Dark Phoenix (2): The Inner Circle - S3-E12
Continuity mistake: When Sebastian Shaw is escorting Jean out of the room, there is a chair with a side table in the foreground. A couple of shots later when Wyngarde is sitting in the chair, the side table has disappeared. (00:06:09)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Xavier is explaining that he challenged the Shi'ar to a duel of honor, there is no-one standing between him and Lilandra, Earthquake, and Gladiator. When the shot changes, Gambit and Beast are now standing between them. (00:02:24)
The Dark Phoenix (2): The Inner Circle - S3-E12
Continuity mistake: When the Dark Phoenix has broken Wyngarde's illusion, and he collapses to his knees, his hairtie has gone from being a blue band to a black bow tie. (00:19:15)
Dark Phoenix (1): Dazzled - S3-E11
Continuity mistake: When Wyngarde first invades Jean's dream and places her down on the bed, she has a mole near her left nostril. Later in the scene when she is looking overboard, the mole is next to the corner of her lips, and even briefly disappears from her face. (00:13:35 - 00:14:23)
Dark Phoenix (1): Dazzled - S3-E11
Continuity mistake: When Sebastian Shaw is asking if the Phoenix destroyed herself, Wyngarde is standing to Shaw's right. When the shot changes, Wyngarde is standing behind the White Queen, directly across from Shaw. (00:07:56)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Lilandra slams her first down onto the control panel, the appearance of the control panel changes between shots. (00:17:14)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Cyclops and Jean are hiding in the shallow alcove, as he is saying there's so much he wants to say to her, his teeth alternate between being white and flesh-colored. (00:13:56)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Lilandra is explaining that it is her duty to protect her people, the band around her elbow alternates between being gray and yellow. (00:06:18)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Cyclops asks Lilandra why she has kidnapped the X-Men, the background shows several sections of people in stadium seating, several yards in the distance. When the shot changes, the background now shows a wall that is very close to her head. (00:03:02)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Storm is questioning why the Shi'ar Imperial Guard have stopped approaching the X-Men, Gambit's pants are colored blue, when they should be black. (00:02:16)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Continuity mistake: When Wolverine says "You got that right," there is no-one standing between him and Xavier and Rogue. When the shot changes, Storm is now standing between the three aforementioned characters. (00:02:03)
The Dark Phoenix (2): The Inner Circle - S3-E12
Continuity mistake: When Wolverine emerges from the dumb waiter and kicks the waiter against the wall, the waiter ends up beneath a painting. When Wolverine walks toward the turkey, you can see the painting on the wall, but the waiter has disappeared from beneath it. (00:07:24)
The Dark Phoenix (2): The Inner Circle - S3-E12
Continuity mistake: When the White Queen is telling Shaw and Wyngarde to think, there is a painting on the wall to Shaw's left. When the shot changes, the painting has disappeared. (00:06:28)