You are probably bumping up against her cervix when you are having sex. Change positions and perhaps not go in so deep.

I agree!!!

She actually likes it when I hit her cervix so I don't know if that is it.

It is painful if hit in the 'right' way. Incredibly painful. Like shooting up through your entire body and you need to double over painful.

This is really really important:
if the pain is that bad and persists make sure your girlfriend gets an ultrasound. Why? It might be an ovarian cyst, which is not a big deal. But the same thing happened to me.

Yes- consistent pain during sex can be a sign of other problems. She should mention it to her gyno. It could be just hitting her funny, (that's happened to me) but it could also be something more serious. You just want to make sure it isn't. Right?