V: The Final Battle: Part 3 (2 Hrs) - S1-E5
Continuity mistake: When the Red Dust is spread, there is a brief shot of some California citizens watching, and we see the Bernsteins among them. But the actress at George Mofogen/Mr. Bernstein's side is not Bonnie Bartlett, who played Mrs. Bernstein in the first two episodes.
The Return of Optimus Prime (1) - S3-E29
Continuity mistake: At the end of the episode 'Dark Awakening', Optimus is seen without an eye and an arm, he also has other damaged points, but at the beginning of this episode, when Jessica and Gregory get to Optimus, he is in perfect condition with no damage.
Give Me Your Princess - S1-E17
Continuity mistake: Commander Keith pilots the blue lion for part of this episode since the princess is trying to learn to fly the black lion. When Keith is transported to the lion it is the black lion.