Blooper

The eye color of Scorponok changes randomly from red to yellow a lot during the first season.

In the second season, Tarantulas calls Megatron's efforts to rewrite history "madness". Yet in the third season, when he attempts to betray Megatron, Tarantulas also tries to drastically change history by trying to destroy the Ark. Of course, he is mad himself, and he could have changed his mind, but his comments contradict his actions.

The size of the characters fluctuates in different episodes.

For a number of episodes in the show's beginning, every time Waspinator transformed, the wasp stripes on his thighs were mapped on the wrong axis. This was only corrected later on.

In the episode "Fallen Comrade", during the fight over the bridge, Waspinator is missing his stripes on his posterior. They are missing again when he and Terrorsaur are attempting to open the stasis pod

At one point, it is hinted at that Dinobot's beast mode is a Velociraptor. Although he does resemble the genetically engineered "Velociraptors" from Jurassic Park (1993), he barely looks like a real-life Velociraptor. Some of his erroneous features could be attributed to him being a robot, however there are still a number of legitimate errors in his appearance: his skull is the wrong shape, for one. He also lacks feathers, though at the time this series was made, evidence of feathers on Velociraptor had not yet been found.

Terrorsaur transforms into a Pteranodon with teeth. Real life Pteranodon didn't have any teeth, hence their name, which means "winged and toothless".

An interesting, yet erroneous design feature of Dinobot are his double-thumbs. He has five fingers on his robot hands, yet his beast-feet only have three toes, even though during transformation, his feet become his hands. In real life, raptors only had four toes. It has to be mentioned, that the toy his cartoon appearance was based on came with six toes/fingers.

Kup, who is on Cybertron while the events of this series are occurring, is visible over Optimus Prime's right shoulder when the Preds break into the Ark's control room.

There is a rigging error on Megatron's season 1 animation model. Every time he bends his legs, his knees distort.

There is an odd rendering error related to Dinobot's rotating shield in some episodes. When the shield is spinning in front of him, the shield's blur effects somehow blot out the shiny metal textures on Dinobot's robot body, making him look dull.

Due to the primitive CGI graphics, the animation suffers from a huge amount of clipping: solid things passing though other objects.

At the beginning of season 2, Rattrap coins the name "Transmetal" in reference to their updated bodies in a private talk with his fellow Maximals. Yet later, characters from both factions start using the term as if it had been common knowledge.

In several occasions, characters who are able to fly fall off cliffs or into crevasses.

Megatron's dragon form is not given an explanation. When Optimus Primal combined with the Spark of the original Optimus, he retained his gorilla mode (his all-time beast mode) and acquired two vehicle modes. But when Megatron combines with the Spark of his namesake, he loses his dinosaur form and gains a dragon form, even though he had no dragon DNA to scan.

Tarantulas' plan in the first season is to capture a stasis pod for himself to get off the planet. At the end of the season, he and Blackarachnia have to break into the Maximal base to acquire a pod and reconfigure it into a flying vessel. It is never explained why he didn't simply use the pod that Blackarachnia came in in the first place.

At the end of the first season, the Vok claim that there will be a great danger if the planet isn't destroyed. This is never elaborated on.

Season 3 establishes that Transformer bodies containing two Sparks go through a radical transformation, gaining new power and growing larger. But in season 1, when Starscream's Spark possesses Waspinator, he doesn't go through any transformation aside from very minor cosmetic changes (like his faction symbol changing from a Predacon to a Decepticon logo).

At the end of the second season, the Tripredacus Council members talk in private about "their" Decepticon ancestors. Yet in the third season, we learn that they are not in fact descendants of the Decepticons.