I'm not sure what the mystery is all about or why everyone is giving their own thoughts on what may have happened. This is a rare case where the woman came out with all of it, seemingly word for word. She was bothered by what happened during the sex, and that is basically that. Only thing you can do is offer her your support and understanding, and probably apologizing to a degree (though from what I read this was sort of a two way street. She had the ability to stop and tell you to put a condom on). If she can't manage to get over what happened, then that's the end of it. Not meant to be. But I wouldn't beat yourself up over this. I don't think you did anything "wrong".
Thank you! Yeah, been a few weeks now since I posted this thread, and am starting to realize that this is probably the major factor.
Granted, there were things I could have done better: post-sex aftercare, cuddling after, disqualifying myself too soon about not wanting a relationship after she sent her text a few days after, insisting on wearing the condom despite her initiating.
I did offer her understanding. And she said she's going to take this time to work on her ability to hold boundaries. Likely there's an ex in the background that's still on her mind, but I can't spend time ruminating on that.
I responded to her as if I took what she said at face value (and no way for me to know, so I did). Gave my respects and understanding. And am now moving on. It didn't end with either of us blaming the other so it leaves the door open in the future, but I'm not waiting for it.