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.
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)Phaneron
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)Phaneron
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)Phaneron
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)Phaneron
Plot hole: This episode showed that Beast was an original member of the X-Men and also depicted the original X-Men battling Magneto. However, when Magneto attempted to break Beast out of jail in the season 1 episode "Enter Magneto", Beast said to him "I don't believe we've met. Magneto I presume."Phaneron