If this puppy truly is from a puppy mill (sounds like it... ) The crate training may not go as smoothly as with most puppies. Often, pups in mills are forced to eliminate in their sleeping area. Once they start doing that their natural aversion to it is compromised. The peeing in bed suggests that.

If that is the case the crate may not be the answer (it's the best way with pups that come from better circumstances though). I'm not sure where to go from there but if she "goes" in her crate...that may be the reason.