Sometimes it's just bad genetic match ups. When I was breeding NZRs I had to import some bucks from an out of state breeder (the local pool was too small after 5 years) and I had nothing but problems with those litters. No deformities, but suddenly litters went from 10+ went to 5 or 6, internal organ failures, stuff like that. Once I removed those bucks from the breeding pool, the litters went back to normal. Sometimes, it's just not a good match despite best intentions.