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.
Deliberate mistake: Identical twins Beverly and Elliot have the exact same beauty mark on their faces, roughly on the smile line directly across from the right nostril. Identical twins don't share features like that.