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 (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)
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 (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)
Savage Land, Strange Heart (1) - S3-E8
Plot hole: When Kazar discovers that Sauron is really his friend Karl Lykos, Lykos reveals that he was turned into Sauron by Mr. Sinister. However, in the season 2 episode Mojovision when Sauron was attacking Shana, Magneto already knew who Sauron was. Magneto was the master of the Savage Land mutates years before Mr. Sinister was and hadn't been to the Savage Land for many years before then, so if Magneto already knew who Sauron was, then it couldn't have been Mr. Sinister who created him. (00:19:46)
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 (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)
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)
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."
Plot hole: Nightcrawler spends a good amount of time trying to escape the angry mob on foot when he could simply teleport away from them. (00:02:00 - 00:02:40)
