It may be that when she wakes up, she's disoriented and therefore scared. Put a night light in her room so that it's not dark when she wakes up. Then, have an extended story time for a few nights.
Sit in the room with her, lit only by the night light (if you can manage it) and tell her stories. Get her used to the look of the room when it's dark, get her used to the idea that she's safe and protected.
This kind of behaviour isn't unusual and will pass over time. I know it's distressing but don't worry about it too much.
One thing.. our youngest son would wake up, upset and crying in the middle of the night. If I tried to comfort him, it would often just make him worse. It became obvious that even though his eyes were open, he really wasn't awake enough to be coherent.
In the end, I learned to go in, let him know I was there and he was safe, then leave the room. He'd grumble and cry for a minute, then would fall back asleep.