Ayon, my Vet says if a puppy is eating mud, it's possible it is deficient in Calcium and other related minerals. The chances of this is even more given the fact she's on home-cooked diet. That's why its adviced if you're feeding home food, you should supplement the diet with some good supplement so that any deficieny arising out from home-cooked diet could be met by the supplement.
You mentioned you're pup doesn't go out of the house. Any reason why?