How do giant robots like Megatron and Soundwave turn into not only a human-sized gun and tape deck, but Cybertronian-sized ones as well?
Where did the Protectobots come from? They just... appear in Bruticus' Revenge and are just there for the rest of the series. No origin, no nothing. Same with the Predacons and Terrorcons in Season 3.
Does Cybertron have an atmosphere? Spike, Chip and Carly have all been to Cybertron with no form of breathing assistance and they move just like they do on Earth, which assumes it has Earth's gravity...
Right in the first episode, Megatron flies out of the sky and lands on an oil rig. Aside from him being incredibly large and as menacing-looking as an 80s cartoon villain can get, why is the first instinct of the human workers to immediately throw things at the giant robot?
The Autobots shouldn't need Teletraan to tell them that Megatron shouldn't have those powers in Heavy Metal War. They've been fighting him for millions of years...
In Prime Problem Megatron's Optimus Prime clone accidentally refers to Ironhide, Prime's second in command, as Bumblebee. Megatron knows who Ironhide is. He has called him by name in a previous episode.
They're actually made of sturdy materials beforehand, so the gold must have just improved it.
There's a reason it's called Gold Plastic Syndrome rather than Gold Paint Syndrome.
Yes, they would have come down with Gold Plastic Syndrome...if they were toys. Why would that problem affect real robots?
Thief In The Night has Six-Gun and Scamper interrogating the Dinobots (and Sky Lynx) about the theft of national monuments like the Eiffel Tower, the Taj Mahal and Fort Knox....did they honestly not realize that, powerful as the Dinobots may be, they were incapable of physically picking up buildings? The fact that monuments were going missing and the dinosaur transform static's consistent presence should have tipped Metroplex off to the idea that maybe Trypticon, the only Decepticon large enough to do such a thing, was behind the thefts; after all, Trypticon has a dinosaur for a robot mode, so he probably has the same dinosaur transform static as the Dinobots and Sky Lynx. The whole "interrogate them due to dinosaur transform static" thing comes off as Metroplex forgetting about Trypticon completely.