Other mistake: When Spike is thrown out of the base by Megatron at the end of the episode, Optimus calls him 'Splik'.
Revealing mistake: When Bumblebee is knocked onto his side, Ratchet kneels down to shove him back onto his wheels. The only problem is that when Bumblebee drives away, the animators forgot to add Ratchet's leg (that was previously obscured) into the frame.
Desertion of the Dinobots (1) - S2-E19
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: Omega Supreme transforms his arm into a rocket and blasts off to the moon, but later, he transforms fully, but he left his body on earth, how was he able to transform?
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.
Other mistake: When the Decepticons shoot the monument at the end, Optimus runs to save it, you can see two Optimuses (Most likely because the animators forgot to get rid of the other prime which is just standing there).
Continuity mistake: At the beginning when Soundwave is attacking the bunker as he ejects his cassettes he says Buzzsaw (the gold condor) but instead ejects Laserbeak (the red condor).
Continuity mistake: Red Alert's door abbreviation has always been an F, then a shield, then a D, but when he is racing through the city when the Autobots are looking for him, he passes them and the abbreviation is: E, shield, D.
The Ultimate Doom: Brainwash (1) - S1-E5
Audio problem: When the Decepticon jets attack the maharaja's palace at the beginning Thundercracker speaks with Skywarp's voice. Later, at their base when the fake Optimus comes out Skywarp speaks with Starscream's voice.
Audio problem: At the end, Inferno comes out from the blaze with Red Alert in his arms, Red Alert then says something, but his mouth doesn't match what he says.
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: Optimus Prime, whose primary color is red, when being tied to a rock alongside his troops during the episode's climax, turns blue for a second.
Continuity mistake: Skyfire's Decepticon symbol changes color throughout the episode. Sometimes it is purple and sometimes it is red.
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.
Suggested correction: They only show Daniel strapped in once, and that's when he sits up & breaks them. All the other scenes they just show his face up close and you can't actually see that he's strapped down.
Continuity mistake: When we see Daniel in bed sleeping he is in his pajamas but when he is kidnapped by the Quintessons he is in his regular clothes.
The Return of Optimus Prime (1) - S3-E29
Other mistake: When the Protectobots combine into Defensor, his right arm is missing.
