I think if you start taking her out every 3 hours or so during the night to go potty.. she will learn that she shouldn't potty in her bed. because as much as my Wookie will want to roll around and sit and lay on his puppy pad, he will never pee or poo in his bed... aka, my bed
he jumps off the bed, which wakes me up.. then i run to take him to the pad.. he goes right away, and comes back to sleep.. im hoping he will soon learn to jump off and go pee on the pad and come back to sleep.
I think making the crate a little smaller with a towel or sponge material or something might help.. but if she is peeing in there, then she clearly needs to go, and cant hold it anymore...
my wookie usually only goes once a night, and hes almost 5 lbs.. if your puppy is smaller, she might have to go more?
but i definately think you need to change the crate set up soon, otherwise, she will think its ok.