Plot hole: After Storm's attempt to escape the Genoshan prison is thwarted, she ends up in the ocean right at the shoreline of the beach, where she is captured by a Sentinel. Aside from the fact that it makes no sense for a Sentinel to be hiding in the ocean in the event that a mutant tries to escape the prison, there is absolutely no way that a two-story tall robot could hide in the ocean right by the beach, as the water would be way too shallow. You can even see that the water level only goes up to the Sentinel's ankle area when it is standing upright in the ocean.
Plot hole: After Wolverine deduces that Colossus wasn't the person who destroyed the X-mansion and Colossus walks away, Jubilee gets a phone call from Rogue literally less than 30 seconds later informing them that the bank was being robbed by somebody big who is later revealed to be the Juggernaut. Wolverine (now wearing a different set of clothes) and Jubilee are then shown arriving at the bank in Wolverine's jeep just in time to see Colossus being arrested for the crime while claiming he was only trying to open an account and stop the robber. If the robbery was being committed while Colossus was fighting Wolverine, then the police and bank employees would have known Colossus was not the perpetrator, not to mention the bank would have been closed off to the public, effectively preventing Colossus from going in to open an account in the first place. The only way Colossus could have feasibly been implicated would be if he was at the bank the same time that Rogue called Jubilee, which he obviously could not have reached the bank in that amount of time since Wolverine had to drive there.
Plot hole: After Wolverine tells Gambit that he only knows how to pick pockets and steal candy from babies, Gambit attempts to retaliate by kinetically charging one of the bricks Wolverine is working with in order for it to blow up in his face. Anything Gambit kinetically charges makes a high-pitched humming sound, and Wolverine possesses a superhuman sense of hearing, so he should not have been caught unaware by it.
Plot hole: When the Leader says "Take me to my car at once!", one of his guards goes to open the door to the room only to have Cable shoot the door with his plasma rifle. The Leader then says "The other way you fool!" and everyone in the room starts running for the windows that Cable shot out a few minutes earlier, which happened to be the only other way out of the room. As evidenced earlier from when Cable shot the windows out, that particular floor appears to be 8 stories up, so if everyone in the room exited through the windows, they would have all fallen to their deaths as all of them were regular humans with no superpowers.
Plot hole: Towards the end of this episode, Jean Grey nearly falls to her death when a concussion blast from Cable's gun knocks her off a cliff, only for her to be saved at the last moment by Rogue. Apparently Jean Grey and the writers for the episode forgot that her telekinetic powers give her limited flight ability as well as the ability to slow falls, both of which she has demonstrated in other episodes.
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: Wolverine bails out on the mission to destroy the files at the Mutant Registration Center to instead go look for Jubilee after she goes missing. When the rest of the team arrives, Wolverine is already there waiting for them. They flew to the Mutant Registration Center in a jet and their mission briefing heavily implied that they needed to leave immediately, so there is no way Wolverine could have arrived before them if he was off looking for Jubilee first.
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