Plot hole: In the season one episode The Cure, when Pyro and Avalanche are in the bar on Muir Island waiting for Mystique to arrive, Avalanche says "This friend of yours better show up soon or I'm going back to jail, just for something to do!" Rogue then comes in and Pyro suggests to Avalanche that Rogue could be Mystique, to which Avalanche responds "What do you mean it could be? Don't you know what she looks like?", leading Pyro to tell Avalanche that Mystique is a shape-shifter. This dialogue implies that Avalanche has no idea who Mystique is, which is further substantiated when Pyro and Avalanche kidnap Mystique later in the episode while she is in the guise of Dr. Adler, and Avalanche didn't recognize Mystique when she revealed her true form. However in this episode it is shown that Pyro and Avalanche were both previously members of Mystique's Brotherhood of Mutants, so Avalanche should already know who Mystique is without Pyro having to tell him. Rogue was also a member of that group yet neither Pyro nor Avalanche recognize her.
Plot hole: After Magneto and Xavier discover that their powers have vanished, Mr. Sinister is shown to be watching them through surveillance footage, zeroed in on their faces from a straight angle. At this point, Magneto and Xavier are standing at the edge of a cliff in the Savage Land, which is a jungle hidden in Antarctica. There's no conceivable way Mr. Sinister could have security footage of them from where they are located. Any camera would have to be mounted onto a tree, and the cliff is at a considerably higher elevation than the jungle itself, as well as a considerable distance away. Even if Mr. Sinister was able to zoom in on them from such a distance, the treeline being lower than the cliff would only allow him to view them from a low angle, and that's only if the cliff wall didn't obscure them. (00:20:00)
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)
'Til Death Do Us Part: Part 1 - S2-E1
Plot hole: The establishing shot of the White House indicates that President Kelly's press conference is taking place there. A member of the Friends of Humanity disguised as a mutant busts into the room and starts terrorizing the reporters and destroying everything. The Secret Service would have either detained or shot this man long before he could have even gotten close to the press conference. Graydon Creed also shoves a security guard that tries to intervene but somehow isn't arrested for it. (00:05:50 - 00:06:35)
Plot hole: After Beast and Dr. Bohlson leave Carly's room, they briefly chat in the hallway just outside the door for less than 15 seconds in real time, and then discover that in that brief time frame, the Friends of Humanity abducted Carly from her second-story room via the window, managed to incapacitate the nurse, security guard and Carly's father, toss around furniture and spray paint "For Humanity" on one of the walls, all without any of the victims making a sound or the Friends of Humanity making a sound themselves. The Friends of Humanity aren't ninjas, rather they are shown to be somewhat bumbling, so there's no way they could have done all that as quickly and quietly as shown. (00:12:30)
