Plot hole: Perceptor discovers that the reason for their malfunctioning is because their Cybertonium has deteriorated after millions of years of being exposed to Earth's atmosphere. The key word here being 'millions'. This explains why the original Transformers who crash landed on Earth (4 million years ago) are affected, but newer characters like Perceptor, Powerglide, Hoist, etc. are affected despite the fact that they have only been on Earth recently.
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.
Continuity mistake: After the Decepticons dig up Skyfire they look at his memory banks to show what happened to him. In the flashback it shows Starscream transforming into his Earth jet mode which he shouldn't have had because it takes place before they all crashed on Earth.
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.