Megatron's gun mode is entirely white as Soundwave grasps him two-handed, right before the first commercial break.
Very early in the story Trailbreaker is colored red when his color is normally dark gray.
As Brawn confronts Starscream and Thundercracker, the Decepticons switch places between shots.
Starscream's eyes are blue as he drags the weapon frame over to Megatron.
When Windcharger flees from Laserbeak, he is drawn like his toy, instead of his cartoon animation model. You can tell, since the back of his car mode is incorrectly aligned with the hood, which was a common issue with his toy.
As Wheeljack encourages Sideswipe, the glow of his right "ear" isn't quite aligned with the ear itself.
When Megatron follows Starscream and Thundercracker out of the pyramid, his Decepticon emblem disappears for a moment.
Just as Skyfire is revealed and there is a collapse of ice, Skywarp is seen sitting in snow for one scene, his nose section in his chest is incorrectly colored white. It should be black.
The parts of Skyfire's tail end that light up as he activates his jets don't actually correspond to his jet thrusters.
Bluestreak's mouth isn't moving as he delivers his "watch the birdie" line.
The Decepticons claim they have found the Crystal of Power among the ancient Incan ruins in Peru. However, the pyramid in which they find the Crystal of Power resembles Chichen Itza (in Mexico), which is distinctively Mayan architecture.
Megatron can destroy the Sky Spy which in low Earth orbit, but can't shoot Optimus Prime when he's 30 feet in front of him.
Skyfire flies back from South America to the Autobot base in North America, picks them up and flies all the way back, yet during all this time, the Decepticons who were already headed for the relatively close-by mining town haven't reached there yet.
The Autobots need to go from the USA to South-America. To do this, they drive all the way up to the Arctic to dig up their pal Skyfire who had been buried under ice a few episodes earlier. Then they use Skyfire to fly them over to South America. If they knew Skyfire was alive all along, why didn't they rescue him earlier? When they do save him, the Autobots uncharacteristically welcome him in a rather unfriendly manner, by telling him to take them to places. Secondly, this route to the Arctic and than way back to South America seems really complicated and time-consuming. They could simply have driven to their destination in the first place. The Autobots are capable to "drive" even on water with their water-skis after all, so a trip to South-America from North-America wouldn't have been a problem for them. No matter how we look at it, their plan doesn't seem to make any sense.
Why would the Incans build such huge stairs that giant robots can easily walk on them? Furthermore, where did the gates that automatically open come from in the ancient temple? The Decepticons are not shown installing them at any point.
While Huffer does state in a previous episode that the Autobots are not fighters like the Decepticons. The whole team still can't overwhelm a Decepticon force consisting of just Megatron, a lone Reflector, and Soundwave and Laserbeak.
When Megatron calls Skyfire away for a job, leaving Starscream and Thundercracker on guard duty, starscream protests and Skywarp tells him to have a good time playing 'crystal nurse' but is incorrectly colored as Thundercracker.
Skyfire knows Wheeljack but they've never been introduced to each other.