Goof (continuity error): In "Reunion", Professor X's gloves disappear for one shot when he is chained to the wall.
Goof (continuity error): In "X-Ternally Yours" Bobby and Belle place their tithe boxes before the X-Ternal, but the boxes disappear in a wide shot.
Goof (continuity error): In "Night of the Sentinels" the tower guard's hair changes from black to brown when Rogue catches him in mid-air.
Goof (continuity error): In the episode "Nightcrawler" Rogue goes from wearing her tattered costume to monk's robes and back between shots.
Goof (continuity error): When Rogue knocks a defiant Wolverine out by absorbing some of his energy, she takes off the yellow glove on her right hand with her left and touches his shoulder. Wolverine then collapses and a scene is shown with a partial close-up of Rogue's body. It shows Rogue's right hand covered with a yellow glove while it is now her left hand that is bare which is still clutching on to the yellow glove which she removed from her right hand.
Goof (plot holes): One of the Sentinels asks "Where are they?" after the X-Men attack their base. The Sentinels should have already been after the X-Men and not asking where they are, considering they can detect and track mutants in a 5 mile radius.
Goof (factual errors): Cyclops uses his optic blast to shoot a gun out of a guards hand. The gun smokes as if there was a sudden exchange of heat. However, Cyclops' optic blast is concussive and transfers no heat.
Goof (plot holes): In the flashback of Rogue learning how to use her powers, she absorbs Pyro's abilities. She then creates a dog made of fire out of thin air. Pyro's ability isn't creating fire, it's manipulating fire. That's why he wears the flame throwers. So there's no way Rogue could have created the dog made of fire with no fire already existing.
Goof (continuity error): Jubilee is shown in the box containing all the X-men for a split second, until it is spun around taking Storm and Cyclops away. It cuts back and she is not there again.
Goof (continuity error): Storm's red comm badges appear and disappear from shot to shot during the battle with Garrok.
Goof (audio/visual unsynchronized): When Sabertooth and Wolverine are grappling in the science lab, their voices are reversed. Sabertooth's mouth moves during Wolverine's lines and vice versa.
Goof (factual errors): The leader of the group that goes after Apocalypse states that the world has had to put up with Apocalypse's evil for 5,000 years. Seconds later he states that Apocalypse has been wreaking havoc for "500 centuries" which would actually be 50,000 years.
Goof (continuity error): Wolverine's uniform tunic is shredded during a battle but in the final shot it's undamaged.