When Soundwave's cassettes eject, Cyclonus seems to be larger than Galvatron, due to the misplacement of his animation cel.
Rodimus is missing his spoiler during one overhead shot in the opening battle.
In one shot on Cybertron, Wingcharger can be seen running around in the background. He had been killed before the season began.
Galvatron's purple Decepticon logo turns red when he calls Trypticon.
Unicron's severed head looks as if it was made out of rock. Normally, it is drawn as nothing more than a head.
As Tornedron in the form of a giant bug steps over the bodies of Blades, Slingshot and Wheelie, its glowing aura is on a lower cel than their bodies, making it appear to pass under them, despite the fact they're lying on the ground.
As the Predacons open fire on the Dinobots inside Trypticon, the firing effect of Headstrong's nose-horn is misplaced. He then moves his head to where he is supposed to be shooting from.
When Grimlock says "Me Grimlock not know where I go.", the animation cel of his lower jaw overlaps his upper jaw.
When Headstrong is blown over, he continues bouncing like rubber for the remainder of the shot.
The Oracle claims Primacron created some of the primitives, which is incorrect. Wheeljack and Ratchet built the Dinobots in "S.O.S. Dinobots (1984)" and "War of the Dinobots (1984)", Trypticon was built by the Constructions in "Five Faces of Darkness: Part 4 (1986)", the Quintessons built both the Predacons ("Five Faces of Darkness: Part 5 (1986)") and the Terrorcons ("Money Is Everything (1986)"), and the "Secret Files of Teletraan II" segment on the history of cassette technology states the Decepticons built Laserbeak, Ravage, Buzzsaw, Ratbat, Slugest, and Overkill, and the Autobots built Steeljaw and Ramhorn.
The Oracle mistakingly calls Sludge "Sweep".