These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
"Distribution." You'll be guessing until the very end who's real and who isn't. And what in the name of Primus is going on. A 'simulation' that's a tournament-style matchup of every 'bot in the series, with robo-catgirl announcers. Some characters who are real walk in and out of things totally unconcerned with who's sitting across the room from them, seeing how they're usually trying to murder each other. Then turn out to not be real, making you wonder what the point of their being in the simulation was at all. Then whoever was just wondering if the guy who just walked out was or wasn't real... turns out to not be real. It was just... the most insanely random thing Transformers has ever done. Bad dubbing takes it from random to incomprehensible and insanely random.
In Superlink, this was a 500th Episode special for the entire franchise, was non-canon, and was shown at a special time. In the dub, to make up for cutting an episode, they added it to the actual run of the show. Right in the middle of a Darker and Edgier arc that was basically all-out war.
Also, they tried to cut out Mirage's crush on Galvatron in the dub, but couldn't completely.
Mirage: But I've been so loyal! How could Galvatron not know how I feel about him?!
Padding: Unicron perishes in "Unicron Perishes," appropriately enough, but then it un-perishes so we can basically repeat the entire plot for 10 or so episodes. On a smaller level, see As You Know on the main page.
Jerkass Woobie: The writers were clearly going for this with Kicker but it just made him even more insufferable.
Starscream is reborn as a confused, and angry spirit/being, up until Megatron gets hold of his mind and makes him loyal. He remains that way without his Noble Demon characteristics that made him famous in Armada.
Demolishor went through a whole arc where he struggled with his allegiance. As Cyclonus and Tidal Wide defect back to their old faction, he tries harder and harder to do the right thing, until, in his penultimate episode, he makes his decision and saves Megatron's life at the cost of his own. He's resurrected in the following episode and is considerably less conflicted and quite a bit stupid, implying Megatron messed with his mind. The arc is never brought up again.
Wing Dagger loses his best friend to Shockblast and then tries to avenge his fallen comrade, performing a Heroic Sacrifice. His quest of vengence is almost never brought up when he is resurrected.
There's some of Unicron in every Transformer. That should really go on to mean something or be important somehow. But this is Energon, so it doesn't.
Kicker wasn't just a Jerk Ass in the beginning: he didn't like Cybertronians because as a kid the whole 'alien robots' thing took up all of Papa's time and once lead to Kicker falling down a really deep hole, and he also just didn't like being told where he could and couldn't go on his own planet while living in an Autobot facility. Hardly earth-shattering, but it's a reason. Rather than have him grow to trust Team Prime in a charactery-developy way, the whole "there's a reason he's this way" thing was just forgotten early on and he spends the later 48 of the series' 50 episodes being rude for no discernible reason. It takes until midseason for everyone else to similarly forget that they don't like it when he's like this.
There was more to it than that. When Kicker developed his energon sensing powers as a child, his father had the bright idea to use Kicker as a living energon detector. For years, he dragged his young,not even a teenager son around space, where he had to deal with a few mining accidents that nearly cost him his life. The Autobots saw no problems with putting him to work like this, and so Kicker grew resentful of both them and his father. This is only brought up a few times, he never calls his father or the Autobots out on it, and by the end of the series he seems to have forgotten about it entirely.
Rodimus, who led a faction of Cybertronians who said Screw This, I'm Outta Here to The Forever War and hasn't been seen in millions of years, returns, and he and Optimus are far from on the same page. Rodimus' team proceeds to... fall in line with Optimus' within two episodes and never really add much to the proceedings.
The Woobie: Demolisher (constantly abused by Megatron and forced into a conflict he wants no part of), Ironhide (constantly abused by Kicker and has most of his friends die), and Wing Dagger (fails to save his best friend and never gets the justice he seeks).