The crate is probably still too big, they need to be no bigger than allowing the dog to turn around and stand up. Joey did the same thing until we put him in a small car seat type of bed. If that is the size it is, then you also need to clean it with Natures Miracle to get all urine smell out, or she will continue to think that is where she is to pee. This includes bedding and blankets as well. When Joey was a puppy, I let him out twice a night to pee. He slept next to me, and woke me, and I placed him on a pee pad in the bathroom, and then back in his crate, eventually it was just once a night, and then he moved to our bed.
I think you are reading too much into it, she probably just has to pee.