You didn't rape her. There's a very good chance she's looking back on the sex with negative emotion and its affecting her ability to see it as happy memory right now.
Some points:
Sexual inexperience and naivety are real issues. Especially for women, as they are often raised in conservative households to believe that sex is dirty, and that enjoying sex makes them slutty. If your ex is new to being sexually active it's quite possible she hasn't worked past that yet.
Her emotional and physical unreadiness wasn't your fault nor your issue. I'm going to assume you were not pushy and that you cared about her enjoyment and consent in the matter. Her feeling bad or weird after sex isn't your fault. I felt weird after the first few sexual experiences with my first boyfriend; it's because sex is a big thing and I hadn't gotten my head around all of it yet. It wasn't my boyfriend's fault.
If she never told you to stop or gave you obvious signs she was upset during sex then how were you supposed to know? You're not a mind reader so don't feel like you should have done something different. I was in an abusive relationship before where my ex would flip shit if I turned him down for sex, so I would never say no. I would however lay there motionless and cry while he went to town. So while I didn't tell him to stop, I do feel that crying during sex is a sign that the sex is not enjoyable and needs to stop.
It sounds like your ex is expressing to you that she wasn't ready for sex, and that it might have been a reason the relationship didn't work out. Don't infer from that statement that she is somehow blaming you or accusing you of being a predator. Sex can be a hard topic to navigate sometimes. At the end of the day if you cared about her enjoyment, and weren't pushy or had to convince her to consent, then don't think of yourself as a villain.