Executive Meddling: Hasbro originally intended the character Overhaul to be called Trailbreaker. This would have given the character the nice transition from Trailbreaker to Leobreaker. Unfortunately, Hasbro's trademark on the name had expired forcing them to rename Trailbreaker, leaving no continuity between the names.
Missing Episode/Screwed by the Network: During its original broadcast in a number of Eastern European countries, the show went off the air before reaching its final episodes, due to the first 16 or so episodes being constantly rerun for months upon months, stalling the series.
The Other Darrin: In the English dub, Megatron's voice actor is different in the pilotnote here played by Trevor Devall, who would later dub Scourge/Flame Convoy in the series proper. (On top of that, he sounds nothing like he would in other episodes. And there's no reason for it: the guy who flawlessly stepped in for Megsy's VA last time the need arose is currently voicing Vector Prime.) Lori is also voiced by a stand-in in three episodes. Override gets the VA pinch-hitter treatment a few times too, but it's quite flawless; if you're deliberately listening for it, her accent (there's a bit of New Yorker in her) is less pronounced in a few episodes.
Ransack and Scourge were also given the same treatment in at least an episode for each. And it's really noticeable in the former's case.