Some animals feel threatened and have random urges to kill their babies because they feel like another animal is trying to do it. Some animals kill their young because they have been "played with" by humans, and have lost the mothers scent. Some animals just abandoned their animals much like some humanity today, because they wish to have freedom again or can't take the constant care. Many animals just have the instinct to take care of their babies no matter what but some just don't take to it very well. It is best to leave an animal and her young alone for the first 2 or 3 weeks at least before you try to play with them, especially if it is a first time being a mother. They need to feel secure to be able to let their young be handled by their caretakers.
My Shepherd's breeder just had a mom dog kill 4 of 8 of her young. The reason she thinks is there was something wrong with the puppies and momma dog killed them. It was not her first litter, I believe it was her 4th or 5th.
I'm not a vet, but I have raised shepherd and have had two litters and have never seen this, although I've heard of it. I'd say the mother just isn't 'cut out' to be a mom and I'd spay her to avoid this in the future.
I would say it is because you are not educated enough to breed dogs. You did not monitor the dog, you did not recognize the signs, you should not be breeding.