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.
Plot hole: When the Quintesson scientist is tricking Cyclonus into going inside his ship he disguises it as a character named Broadside who then says that he has come to take Cyclonus to see Galvatron. The problem is, Broadside is an Autobot yet Cyclonus simply walks inside without any reaction. Most likely the writers intended it to be Astrotrain but wrote the wrong name down.
Continuity mistake: When the Quintessons have Daniel he appears to be strapped to an examining table but the strap changes in between shots. Sometimes it is on his chest but it later moves down to his stomach area and up to his chest again. Another scene shows his legs being strapped down as well but the strap seems to disappear.