Well this could be a result of many things.
It could be that the mother had a genetic disease of some sort which spread to the pups and killed them at a young age. It wouldn't be uncommon.
It could be diet, or they could have contracted some sort of disease.

If they look healthy though they may not have a disease. When I've bred mice and rats, some of the litters die. If it was one of her first 2-3 litters that could have had an effect on her too. Or lack of nutrition.

Good luck with your next litters though.