Factual error: When Moira is calling her ex-husband Joe in Edinburgh from the Blackbird phone, she dials a typical U.S. seven-digit phone number (it looks like she dials 555-1238). However, even assuming she wouldn't be required to dial an exit code from the Blackbird, a typical Edinburgh phone number would have more digits, along the lines of +44-131-XXX-XXXX. (00:16:50)
Plot hole: Magneto states that he went to Washington, DC to witness Senator Kelly's assassination. But Magneto had no way of knowing about the assassination plot. Mystique was the one who was attempting to assassinate Kelly, and Apocalypse was the one who carried out the order. At this point in the show, Magneto had not worked with either Mystique or Apocalypse, and it's highly doubtful that Mystique would leak the plot, since it was supposed to be covert.
Plot hole: When Jubilee and Iceman are tied up, Jubilee has metal "mittens" over her hands that prevent her from using her powers to escape, but Iceman notes that they failed to learn about his powers and uses his ice powers to break free from his ropes. Iceman was in his ice form when X-Factor attacked him and Jubilee, and they also know that he previously attacked their compound, so they should have known that he had those abilities. (00:13:40)
The Dark Phoenix (4): The Fate of the Phoenix - S3-E14
Plot hole: Jean Grey decides to wear her original X-Men uniform in her trial-by-combat. But how could she possibly have had the uniform with her? She wasn't wearing it when the X-Men were suddenly and unexpectedly abducted by the Shi'ar and taken into outer space, and the Shi'ar weren't about to let Jean go back home and grab it. (00:07:10)
The Dark Phoenix (3): The Dark Phoenix - S3-E13
Other mistake: When Professor X says "We must do all we can to defeat the Phoenix within her," there is a black spot that moves vertically across the screen as the camera is panning from Cyclops to Wolverine. It's as if there was a small bug on the lens. (00:11:00)
The Dark Phoenix (3): The Dark Phoenix - S3-E13
Plot hole: When the X-Men are on the roof of the Hellfire Club confronting the Dark Phoenix, Beast suddenly has some kind of hi-tech backpack-like device, despite being held captive without it in the previous episode, and never shown having one when he entered the club in the episode that preceded that one. (00:03:00)
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)
Other mistake: When Apocalypse is holding Rogue upside-down, her belt remains in place despite the fact that her belt is wider than her waist and abdomen (it is not as wide as her hips which is why it remains in place when she is upright). Her belt should have fallen down to underneath her breasts. (00:11:50)
The Phoenix Saga (5): Child of Light - S3-E7
Audio problem: Storm's mouth is completely closed when she says "The immediate threat to New York City has been averted." (00:12:10)
The Phoenix Saga (4): The Starjammers - S3-E6
Plot hole: Rogue is able to punch Gladiator and knock him off his feet, yet in the previous episode when the Juggernaut punched Gladiator he didn't even budge. The Juggernaut is a lot stronger than Rogue, so either Juggernaut's punch should have affected Gladiator or Rogue's punch should not have. (00:17:55)
The Phoenix Saga (2): The Dark Shroud - S3-E4
Plot hole: After Professor X crashes his mini-jet onto the hospital roof and loses consciousness, he isn't discovered until Jean mentally locates him. An aircraft crashing on the roof would cause enough noise to immediately alert staff and anyone else in the hospital of his predicament. (00:09:15 - 00:15:45)
The Phoenix Saga (4): The Starjammers - S3-E6
Plot hole: Corsair takes out the X-Men by having Raza calibrating their stun weapon to humans. Since Corsair is also a human, the blast renders him unconscious along with the X-Men, and the Starjammers take him away. When Wolverine and Phoenix regain consciousness, they realize that Cyclops has been taken by the Starjammers as well. The problem is since Corsair was unconscious, he couldn't have possibly ordered the Starjammers to take Cyclops with them, and the Starjammers had no reason to take Cyclops of their own volition. Raza even acknowledges that Corsair is the one that takes Cyclops. (00:08:15 - 00:09:00)
The Phoenix Saga (2): The Dark Shroud - S3-E4
Plot hole: Wolverine's enhanced sense of smell should have alerted him to Erik the Red's spy on the roof. Failing that, the video feed Erik the Red is receiving from the spy shows Wolverine, Beast and Professor X looking right in the spy's direction, so they would have seen him. (00:15:55)
Other mistake: Ka-Zar refers to Xavier by name despite only having just met him and Xavier never telling him his name. He even asked Xavier who he was only moments before. (00:09:19 - 00:10:17)
Mojovision - S2-E11
Plot hole: Spiral comes into the Earth dimension through the multiple television screens, teleports all X-Men members present to Mojoworld, and then retreats back into Mojoworld herself the same way she left. When the action shifts to Mojoworld, Rogue is among the captive X-Men despite the fact that she was not among the ones Spiral abducted. (00:07:10 - 00:08:05)
Time Fugitives: Part 1 - S2-E7
Factual error: Costumed superheroes notwithstanding, Bishop wouldn't be allowed to bring his gun into the United States Capitol. (00:14:40 - 00:16:10)
Continuity mistake: When Pierre is waiting for Gambit in his boat, there is another boat next to his. When he and Gambit take off, the second boat has disappeared. (00:07:55)
'Til Death Do Us Part: Part 1 - S2-E1
Continuity mistake: Beast disarms a member of the Friends of Humanity whilst perched on a street lamp. When the angle changes to a wide shot, Beast is much higher on the lamp post and would have been too far out of reach to disarm the man in the first place. (00:11:45)
Answer: Chris Potter, the original Gambit voice actor, did indeed quit the role in the 4th season. His last episode was The Phalanx Covenant Part 1 so it seems reasonable that Fox would limit the use of the character even though it was recast. It doesn't appear that Potter left the role due to animosity, he stated in an interview that he wished to play Gambit in the first live action X-Men film.
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