We've never had any mothers do it, but I have heard of mothers having their babies on the cage floor instead of in the nest box. She may just not be a very good mother. Did she show any signs of wanting to build her nest? i.e. cramming hay in her mouth and arranging it in the box? No fur in the burrow is basically a death sentence for babies. They need the fur to survive since they have none themselves. We have a doe that goes ridiculous with fur pulling so we always take a bit out to save for future kits that maybe don't have enough. If it were me, I'd probably give the doe one more chance at breeding and if it doesn't work out then cull her. That way you know if it was a fluke or not.