The Phoenix Saga (3): Cry of the Banshee - S3-E5
Revealing mistake: When Professor X is telling Juggernaut that he is in his mind, if you look closely you can see there is a disembodied mouth on the right side of Professor X's face that is synchronized with his dialogue. Apparently an animation error. Note: this error may only apply to the DVD version of the episode, as it does not occur on the version of the episode that appears on Disney+. (00:04:00)
Revealing mistake: When Beast states that it appears safe to enter the alien ship, his right arm and right leg completely pass through Professor X's body and hover-chair respectively. (00:13:45)

The Phoenix Saga (1): Sacrifice - S3-E3
Revealing mistake: After the X-Men rescue Dr. Corbeau and retreat back to the shuttle, they come upon a room with crew members passed out on the floor. Keep an eye on Wolverine in the background on the right side of the screen and you will see him literally walk through a door panel. (00:17:28)
Answer: Chris Potter, the original Gambit voice actor, did indeed quit the role in the 4th season. His last episode was The Phalanx Covenant Part 1 so it seems reasonable that Fox would limit the use of the character even though it was recast. It doesn't appear that Potter left the role due to animosity, he stated in an interview that he wished to play Gambit in the first live action X-Men film.
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