SureAI

So I finally managed to finish the game, after countless crashes. And what a story wow!. It's even more surreal than Nehrim. A storyline like this one is rare I would say, it really left me thinking. There's one thing bugging me though. In the end I chose to destroy the machine but apparently there was no goodbye kiss. I am confused and it left me a bit bitter because I did everything to get on her side so I don't know where it went wrong or where I messed up. .I don't believe I ever said anything about Jespar so that shouldn't be it. Are there more places where you can mess up the romance because I really don't know. The only thing she didn't like (MAYBE one more thing if so I wouldn't remember) was when I chose not to punish the famer in the excavation site.

If you didn't have a romantic encounter on the airship, then it's too late.
The crucial point is when you get woken up by Jespar or Calia (depending on who has more sympathy for you at this time) after your last Daddy-dream and get asked how you feel about the other.
If you want a romance with Calia...

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then if Calia asks about Jespar, you must tell her you feel friendship for him,
or if Jespar asks about Calia, you must NOT tell him you feel friendship for her.

What is the romantic encounter? On the ship we hid from the Starling in the secret engine room.

I got woken up by Calia and I remember she asked me something about Jaspar, not sure if Jasper asked me anything. I believe I said we're colleagues or something. So if I did not explicitly tell her I feel friendship for him, all I did is rendered void? That's pretty lame if you ask me you wouldn't even think you had to say that. One small thing irrelevant answer changes everything even though you did everything you could to make the option available. Those answers were pretty vague I had no idea.

Yes, there you have the option to go full romance. Either you missed it, or it wasn't there because of the earlier choice.
Did you talk to Jespar before or after you were with Calia in the engine room? The last one you talk to should have the romance-option.
You have exactly 2 options, how you feel about Jespar:
1) We're friends (Jespar->friendzone, Calia->romance-option)
2) Can't say yet (Jespar->romance-option, Calia->friendzone)
(analogous for Jespar asking about Calia)

I didn't know we can actually miss the romance elements! I must learn how to do that on my next playthrough, which I intend to be a jerk.

Well, if you don't get enough sympathy, you won't have any of these options at all, and nobody will ask about your feelings, that's not hard to achieve