Deliberate mistake: When the news program is discussing Gyrich's assassination attempt on Xavier from the series finale of the original animated series, he's shown to have his classic look of auburn hair and sunglasses. However, when this scene occurred, Gyrich had black hair and was not wearing sunglasses. This was done deliberately to match the character design of the original series prior to the final 6 episodes, when Saban took over and redesigned much of the show's look.
Bright Eyes - S1-E7
Other mistake: SPOILER: Gambit's funeral is taking place in his hometown of New Orleans, as evidenced by the coffins being above ground (because New Orleans is at or below sea level). However, Gambit's coffin is oddly lowered into the ground.
Continuity mistake: When Wolverine is telling Morph that Scott and Jean will be leaving the team after their baby is born, the toothpick in his mouth swaps sides.
Tolerance Is Extinction - Pt 2 - S1-E9
Trivia: When Cable scoffs at the uniform Cyclops gives him to wear, Cyclops asks if he was expecting black leather. This is a reference to the first X-Men film, when Wolverine scoffed at the X-Men's black leather uniforms, only for Cyclops to ask him if he preferred yellow spandex instead.
Trivia: Jennifer Hale is taking over the role of Jean Grey from Catherine Disher. Hale previously voiced Jean Grey in Wolverine and the X-Men. She also previously voiced Felicia Hardy/Black Cat and Julia Carpenter/Spider Woman in the 90's Spider-Man and Iron Man animated series, respectively, which take place in the same continuity as this show.
Trivia: Alyson Court, who voiced Jubilee in the original series, opted not to voice Jubilee again so that an Asian voice actress could take over the part, who was later revealed to be Holly Chou.
Remember It - S1-E5
Valerie Cooper: Most other nations don't allow a terrorist to be their leader.
Magneto: Yet so many allow their leaders to be terrorists.
Mutant Liberation Begins - S1-E2
Madelyne Pryor: [In labor pains] Logan, he's, he's here!
Wolverine: Who? Apocalypse?
Madelyne Pryor: The baby!
Wolverine: Oh, crap!
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