Well in my experience I sometimes can't pick up on social cues. Sometimes I can tell people aren't comfortable (socially) but don't know why. I feel like this tendency could be a LII or at least poor Fe/Fi related thing? Seems like something IEEs and SEEs I know don't do. IEE more so than SEE.

It would also be related to Aspergers too. Gulenko has said that LIIs who don't improve their Fi skills may seem somewhat autistic, so Aspergers and LIIness may reinforce this.

My approach has been to be burned by it, and try to not make the mistake again. Because our Fi is 2D, our understanding of it is often limited to norms and rules. (In theory) the way we're supposed to deal with this is that when things go wrong, we make a new rule and try to stick to it. It won't be perfect, and we'll still be blindsided by something else hint-related, but we'll at least be better.

If I were you now, LII a LII, I would either do two things.

Wait, did I just do that thing where I gave people advice when they didn't want it? Oops, better put a spoiler around that.
I won't speak to whether the hints were subtle or not, mainly because the way you've written them they seem clear enough, but hindsight is 20-20 even if you're Maritsa and you don't have Park's glasses.

OPTION A
Go back to the manager and (awkwardly, because we're LIIs so it will be awkward) tell her:
  • That you know the conversation was difficult for you both,
  • You still really enjoy your work,
  • You're sorry you didn't work out at that specific library but that you'll be trying to improve, and
  • She should feel comfortable to give you feedback.

First point is to let the manager feel safe - you're not gonna like shout at her or accuse her of being unfair. If she feels unsafe then she may say something upsetting to you which she doesn't mean.
Second and third point is because I think a manager prefers an earnest employee cos those are harder to find. Hopefully this will buy a few extra lives in case you slip up again in the future.
Fourth point is to hopefully encourage the manager to be really explicit with feedback. On their end, she may have previously felt uncomfortable pulling you up on things you didn't realise.

OPTION B
I would be upset and my self-esteem disturbed. I wouldn't feel comfortable going to the manager to say all that was said in Option A. I would probably write an email or something just because I think it's something that ought to be done. However, I would probably need warmth and friendliness and general closeness with someone to help me feel less uncertain of myself. That could be here on 16types, or it could be other people you know?, but hopefully they would help to build you back up.

And then you'd probably best think of some 2D Fi rule to make sure that this doesn't happen again, like I discussed above.