Goofs

The Autobots can all be seen to fly (much like the Decepticons). Later in The Return of Optimus Prime: Part 2 (1987), Galvatron states that Autobots cannot fly. The only exception to this rule is if they turn into aircraft.

When the Autobots are spying on the Decepticons, Soundwave is colored red instead of blue. The colorists must have mistaken him for the Autobot Sideswipe.

Shockwave is drawn with two hands. His left hand is supposed to be a blaster.

As the camera pans through the battle scene aboard the Ark, we can see two Soundwaves in two different places.

As Soundwave produces the Energon cubes out of his chest, his head is miscolored.

The narrator begins with, "many millions of years ago, on the planet Cybertron, life existed, but not life as we know it today..." yet most of vehicle designs are from 1980s, and Soundblaster is an '80s-style boom box with a cassette tape.

The Autobots and Decepticons originally have Cybertronian vehicle and object forms. However, after crash landing on Earth, their bodies are damaged. The Ark's computer, Teletraan One, releases Sky Spy, a small satellite-like drone to scan vehicles and objects from current day Earth and uses this information to rebuild the Autobots and Decepticons into these new forms.

In the erroneous shot in which two Soundwaves are seen, the arm of the second one isn't completely drawn for a couple of frames, so instead of a hand, he has a huge blotch of gray paint extending from his arm.

When Optimus Prime takes over the controls from Jazz, Jazz seemingly flies out of his seat by himself (faulty animation). In the following shot, the controller is seen having a fully different shape than before, looking much like a pair of antlers.

The shot of Optimus Prime pointing towards the oncoming attack is shown twice, even though at the second time, Megatron's voice can be heard.

The ring of fire for a moment overlaps Wheeljack's animation cel, when it is supposed to be in the background.

When Rumble cracks the ground open with his pile-drivers, the crack's animation cel doesn't move in unison with the background, so for a short moment, it overlaps a mountain.

When Soundwave announces that the Autobots are ready to launch, he isn't moving his mouth-plate.

The Transformers reach Earth seemingly within a matter of minutes, which would be wholly impossible. It is never shown that they are capable of traveling through hyperspace.

The Decepticons leave the Autobots' space ship behind to go looking for materials to build a news space ship out of. Why don't they simply loot the Autobot ship?

We learn later in the season that Spike isn't old enough to hold a drivers license. Why and how then is he working on an oil rig at such a young age. Is he a high school drop out, and his Dad pulled some strings to get him that job.

Soundwave is at first seen turning into what looks like a lamp-post near the Autobots' base. It is never explained, nor even touched upon how nobody notices that one of the posts is missing when he leaves.

After Hound falls off a cliff, the rest of the Autobots haul him back up, even though their base is on the ground, so they would have to go back down anyway.

One of the Decepticon Seekers that Wheeljack and Bumblebee encounter reacts to their appearance with saying "Autobots!". However only Wheeljack can be seen (Bumblebee is inside of him), so he should have no way to know that there are more than one Autobot present.

Skywarp chases after Wheeljack and Bumblebee, even though he could easily have used his teleportation power to get them.

After Hound goes off the cliff, some the Autobots arrive to get him back up. Cliffjumper yells 'Hauler, pull him up'. The Autobot crane that pulls him up is called Grapple, not Hauler.