theory : zett the grandpa mimiga told quote that the doctor kidnapped young mimiga. so it was a red line for quote
Interacting with Zett is completely optional throughout the entire game though, so Quote can come to this conclusion much earlier in the story.
The initial traumas that quote would've witnessed having seen Toroko get kidnapped would've been more than enough for most people, a robot with the capabilities of Quote should've been able to tell something's not right the moment they were threatened with assault by Balrog and Misery (who claim to work for The Doctor)
The initial transmissions quote recieved at the start of the game were SOS calls effectively, so Quote is likely only programmed to help people at his core, and through his interactions with others his definition of "Helping people" has to be constantly redefined in order to save needless violence. Jenka tries hammering this into Quote's head just before he meets The Doctor, but appears to be too stuck in shock/horror watching what The Doctor is doing to Toroko to actually take the initiative of killing him then and there.
If Quote was able to properly infer what Jenka was talking about ahead of time, The Doctor would never have been able to use the flowers against Toroko, let alone anyone else.
But he isn't able to, because Jenka spoke in euphamisms and vagueties and ironically enough the person who helped Quote and Jenka get moving in a timely manner was Balrog, who, while still carrying out The Doctor's orders, was taking advantage of what he knew about both of their behavior patterns to exploit the situation for himself.
theory: droll the born of earth guard hit quote on his head unlocking that feature (prof booster the creator of quote wanted him to study the life in the island)
There's no proof to either of these. But Quote being able to understand the Mimiga, humans, cthulhu, etc. should be enough to tell you something's up.
Do we know that the Mimiga had the same native language as everyone else? How did the humans even learn to speak with them?
There's a lot of history on the island, I think the language barrier broken must've been a
Recent Technological Development that allowed for them all to speak to eachother, hmm.
theory : balrog is holding back to not kill quote because he wanted a friend
Considering Pixel was developing the entire beta version's story around Puu (later known to become balrog in the final game) and his ability to grow progressively stronger in comparison to Quote (who follows the same exact route), I think the final game's arc with Balrog is meant to be Balrog and Quote coming to an understanding that they'd both destroy eachother if they utilized their strength this way.
Balrog knew that the Demon Crown was controlling him and limiting him to the island, and he knew that Quote wasn't under the influence of the demon crown considering his willingness to actively converse with him when Misery was otherwise too busy/apathetic to talk otherwise.
You could maybe consider Puu Black's inclusion in the final game as a nod to how Puu existed in the beta and what arc he was supposed to follow, and how Quote having to defeat Puu Black before his final confrontation against Balrog may have been a euphemism for "Putting to rest the idea of constantly escelating conflict between two machines and using their shared knowledge and power to take down The Doctor". Machines always work in binaries, but if they work with different sets of binaries suddenly they're able to come to new conclusions outside of those binaries.
Also mods move this to the theory section??