Okay I'm dying to know the context
These are the two I spotted, but there may well be more because... well. Beast Wars being Beast Wars. (It is one of my very favourites.) Spoilers below for G1 and Beast Wars, and also one major spoiler for Beast Machines.
"Attack of the Autobots" / "Dark Designs"
In the G1 episode "Attack of the Autobots", a couple of Decepticons make themselves invisible (??) with their invisibility spray (!!!) and sneak aboard the Ark. Do they murder the Autobots on their recharge slabs? Haul them off as prisoners? Take over the ship? No, of course not! They do the very sensible strategic thing and reprogramme the Autobots' beds to make them evil.
The Autobots wake up with red optics and a craving to go out and ne'er-do-well, and immediately place themselves under Megatron's command and start wrecking shop on his orders, until Bumblebee cures Optimus Prime with the power of hugs.
I swear, sometimes if it weren't for TFWiki I'd think I hallucinated all of G1.
Beast Wars revisited this in the episode "Dark Designs", where Rhinox gets captured and reprogrammed to be evil. Now, this already makes more sense than the G1 version: the Predacons barely pull this grab off at all - it's not like they could have done anything to the Maximals and opted for this - and with the number of soldiers on either side of the conflict in the single digits, this is a situation where Megatron turning a single Maximal could make a real difference to the war. But more importantly, "Dark Designs" pretty much centres on Megatron learning firsthand what every viewer of "Attack of the Autobots" over the age of four was probably yelling at the screen: TURNING EVIL DOESN'T AUTOMATICALLY MAKE YOU A LOYAL MEMBER OF TEAM BAD GUY. Megatron chooses Rhinox for his strength and intelligence, and then is shocked, SHOCKED I TELL YOU, when Rhinox pretty much immediately comes up with a scheme to topple Megatron and rule the Predacons himself.
He gets damn close, too. Closer than Starscream-alike Terrorsaur does in his entire season on the show.
"Dark Designs" is a genuinely great episode. It ends with a lighthearted scene where Rhinox describes being a Predacon as feeling like "three gigabytes of attitude on a two-gig harddrive" and everybody laughs, except Dinobot whose culture he just maligned - but, more chillingly, what happens to Rhinox here ends up presaging his conversion into the Predacon general Tankor in Beast Machines.
"A Prime Problem" / "Double Dinobot"
"A Prime Problem" is one of my favourite terrible/wonderful G1 episodes. In it, Megatron clones Optimus Prime* and then has Laserbeak knock the real thing off a cliff, so Megatron can remotely pilot the clone back to the Autobot base. Of course, the real Optimus isn't out of commission for long, so he stumbles back to base, and the Autobots are AGHAST! How will they ever figure out which one is the real Optimus???
This would be a genuinely perplexing dilemma were it not for the fact that Megatron has been paying approximately no attention to any of his opponents but Optimus for the last nine million years. Supremely on brand, no notes. :D
So you've got Optimus #1 going, "My dear friends, I am so relieved none of you were injured during the battle," and Optimus #2 going:
"YOU'RE ALL A BUNCH OF GOOD FOR NOTHINGS, GET BACK TO WORK, BUMBLEBEE!"
and the Autobots give this extremely perplexing conundrum A Lot of thought, and come to the following conclusion:
So they have a race. And the two tie. And a shooting contest. And the two tie. Because they're physically identical but one of them doesn't know who Ironhide is I just aaaaaaahhhhhhhh.
"Double Dinobot" is basically this same ploy done with a dash of intelligence (and a lot of Frankenstein jokes around the cloning but that's by the by :D). It sees Megatron create, not a remote-control shell, but a fully sentient clone of his former-lieutenant-turned-Maximal-traitor, Dinobot. In this version, the clone does actually do his homework, and manages to deceive the Maximals while the real Dinobot is off stranded somewhere. The clone even comes very close to getting Rattrap killed, throwing a temporary wrench in the works of his and the real Dinobot's slowly blossoming trust and love story. It's actually kind of heartbreaking, because a few of the Maximals automatically assume Dinobot's changed his loyalties again. This episode also pulls off a delightful scene where, instead of the clone pretending to be the real Dinobot, the real version pretends to be the clone and contacts Megatron, luring him to the Maximal base.
And then Dinobot eats his own clone, which is... wow. Okay. Huh.
*Pity he never thought to combine this technology with the invisibility spray from "Attack of the Autobots", because I tell ya, few things turn the tide of a war like armies of invisible clones.
