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.
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.