Goofs

Multiple times throughout the series, animators would incorrectly use the CGI models of a normal Cycle Drone to represent Thrust. You can spot the difference because the drones lack the yellow decorations that characterize Thrust.

An important plot point in the series is scanning the DNA of animal fossils. Fossils don't have DNA.

In numerous episodes, lights, laser bolts, explosions, smoke and fire behave like solid objects. In some cases, light rays even cast a shadow which would of course be impossible.

Megatron's virus reverts the Maximals into their original bodies from the first season of Beast Wars: Transformers (1996). However, Optimus Primal should technically be in his Transmetal design from season 2, since his original body was destroyed and his Spark was placed in a new body. The virus couldn't have devolved him further than his Transmetal form, because that was his new body's original form.

After he reformats Nightscream, Optimus remains weakened for several episodes. This doesn't happen when he later reformats Botanica.

Optimus' reluctance to free the Sparks of Cybertron's people before Megatron is defeated for good makes no sense. He fears that if they gave the Transformers their bodies back, Megatron might rob their Sparks again. Actually, if they freed the Sparks and reanimated the Transformers, they'd have an enormous army at their disposal, who'd help defeat Megatron in no time.

Due to their Technorganic bodies, the Maximals have to stay focused to remain in robot mode. But why does Megatron turn back into his beast mode whenever he loses his cool? He isn't Technorganic, so he should have full control over his forms.

After landing on the planet and getting attacked by the Vehicon armies, why do all of the Maximals try to simply run in their relatively slow robot modes? Optimus and Silverbolt could have flown away to safety, and Cheetor was also faster in his cheetah mode. Nor do they fight back, despite possessing weaponry.

When Nightscream offers fruit to the Maximals, Cheetor matter-of-factly states that they only consume Energon, but Optimus suggests that their Technorganic bodies may be able to consume regular food too. However in the previous series, Beast Wars: Transformers (1996), the characters were shown eating fruit and meat a number of times.

Optimus' assertion that the Beast Wars were actually an initiative by the Oracle to bring organic life back to Cybertron makes little sense, considering that the war only started because Megatron stole an ancient artifact from Cybertron to fulfill the orders of the original Megatron. The Oracle had nothing to do with it.