I don't think you did a thing wrong. It's possible she "took it the wrong way" as far as chocolates being traditionally a love/dating gift (though IMO that would be a stretch...but it's possible), or that she doesn't like chocolate, or simply that she's a person who's embarrassed by generosity. Let us not forget that NTs aren't socially perfect either. I think we have a tendency to think that every NT has social situations all wrapped up. If that were true there wouldn't be thousands of articles out there, written for NTs, about how to act in social situations. They screw up more frequently than you might think.
She may not have been raised to be polite, for instance (not saying this is true, just giving an example) - the polite thing to do if, say, she doesn't like chocolate would be to JUST SAY THANK YOU and then move off with the chocolate and then PRIVATELY give them to a friend (who doesn't work with you), donate them or even toss them, but not to make you feel uncomfortable about it.
NTs aren't perfect. You did a nice thing. Giving small tokens is actually a pretty normal, usual thing to do when someone has helped you out. For instance, if your buddies help you move house, it's pretty traditional to give them a 6-pack or invite them to a barbecue or something.
I would say if this happens in the future, give a neutral, small/inexpensive, token gift, like buy her a coffee and bring it to her and say "I just wanted to say I appreciate that you drove me to work on those days. If you need a favor in the future, let me know" and leave it at that.