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.
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.
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.
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.
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 - 00:09:00Phaneron
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."
Audio problem: When Wolverine says to Sabretooth "You taught me that you can't count on your friends," Sabretooth is the actually the one mouthing the last three words. And when Sabretooth says "I saved both our lives you..." Wolverine is the one mouthing the entire line.
Continuity mistake: When Rogue is attempting to rescue Gambit from the avalanche, Gambit's right hand goes from being gloveless to gloved. There is even a point when she is pulling him out of the snow that a glove instantaneously materializes on his hand and then disappears just as quickly.
Other mistake: During the "Previously on X-Men..." segment before the show's intro, it shows the Juggernaut landing in the ocean and walking across the ocean floor after Gladiator had hurled him away. However, Juggernaut's fate was never actually shown after Gladiator threw him. He was only seen fading off into the distance.
Other mistake: When Corsair is running towards the Starjammers and Storm at the top of the Mayan structure, Lilandra can be seen among the group despite the fact that she was not in the episode before or after this moment. This was most likely supposed to instead be Jandra, the Shi'ar child that the Starjammers were trying to protect.
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.
Continuity mistake: When Iceman steps onto the containment field platform, Professor X moves over right next to him, hovering over the platform himself. When Professor X activates the containment field to trap Iceman in place, Professor X is suddenly away from the platform.
Character mistake: When Beast discovers that Iceman has escaped from the containment device, he takes several steps in the room before he even realizes that Iceman is gone. The device was not obscured by anything, so Beast should have realized as soon as he entered the room that Iceman was gone.
Character mistake: When the two security guards are arguing over whether heat or humidity is worse, one guard says "It's midnight, and it's still 97°." However, moments before that the same security guard checked the temperature on his computer and it indicated it was 85°.
Continuity mistake: Professor X's usual hoverchair was destroyed by the Dark Phoenix in the previous episode, so the Shi'ar gave him a new one to use on their starship. However, when Professor X is lamenting over the X-Men's imminent defeat against the Shi'ar Imperial Guard, he is back in his original hoverchair. Towards the end of the episode, he is back in the Shi'ar hoverchair.
00:04:10 - 00:13:15Phaneron
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.
Continuity mistake: When Beast says "We appear to be at the mercy of our hosts," he is noticeably further away from Cyclops than he is from the rest of the episode. The captive X-Men are chained to the floor with not much slack, so he could not have simply moved away from Cyclops on his own.
Continuity mistake: The rubble that Storm is buried under magically removes itself from her. Rogue could not have been the one to unbury her because the rubble falls at the same moment Rogue arrives on screen, and Storm could not have done it herself because she was unconscious.
Continuity mistake: When Storm breaks off communication with Beast, the animation suggests that she is removing the communicators from her chest, but they remain in place. A couple of shots later, they are completely gone. They then reappear and disappear throughout the rest of the episode.
Continuity mistake: When Beast contacts Rogue on her wrist communicator, you can see she is wearing the usual yellow gloves, green sleeves and brown jacket of her uniform. When the shot changes, she is wearing the long-sleeve blue shirt without gloves that she was wearing earlier in the episode.
Continuity mistake: At the very beginning of the episode, Sauron can be seen wearing the necklace of Garokk. Not only is he not wearing the necklace a few shots later, but he isn't even supposed to have the necklace until a few minutes later in the episode when Zaladane gives it to him after he reverts to his human form.
00:01:05 - 00:04:10Phaneron
Other mistake: When the X-Men and Corsair encounter D'Ken in the hallway, D'Ken, Gladiator and Lilandra remain in the background while the X-Men and Corsair are wiped from the screen. It's as if this was meant to be a zoom in on D'Ken, Gladiator and Lilandra, but their size relative to the camera remained the same and the X-Men and Corsair are simply removed from view.
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.
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
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.
Revealing mistake: When Professor X is telling Juggernaut that he is in his mind, if you look closely you can see there is a disembodied mouth on the right side of Professor X's face that is synchronized with his dialogue. Apparently an animation error.
Continuity mistake: When Wolverine is trying to get to Professor Oyama, he slashes twice at the door leaving six claw marks. When the door is shown again after Wolverine is reacting to the explosion, there are suddenly several more claw marks without him ever slashing at the door again.
Continuity mistake: The three tear marks in Wolverine's uniform from when Lady Deathstrike slashes him change position several times. When she first slashes him, the tear marks appear on his chest. Other shots show the tears to be closer to his abdomen.
00:13:50 - 00:16:00Phaneron
Continuity mistake: When Gambit is warning Wolverine that Leech's message could be a trap, the backboard of the basketball hoop is visible over his left shoulder. When the shot changes to Jubilee offering to help Wolverine, the backboard is visibly larger.
Revealing mistake: After the X-Men rescue Dr. Corbeau and retreat back to the shuttle, they come upon a room with crew members passed out on the floor. Keep an eye on Wolverine in the background on the right side of the screen and you will see him literally walk through a door panel.