
Most of my bitches will continue to eat the pups doings while they are in their puppy pen, and anytime they do it indoors, outdoors I usually manage to get to it first.
I would not consider it normal for a bitch not to clean up all the pups waste until at least the time they can move away from their bed too poo unaided, as until then pups cannot poo without the bitch or person stimulating them to do so. If a bitch of mine did not clean her pups after the first day, then I would not breed from her again.
After all in the wild that is the only way of keeping the nest clean, and to help avoid predators finding them.
Poor mothering instincts are often found in toy breeds who appear to have become more infantalised than most breeds.