I don't know all the reasons that could cause it but every now and then a particular pair of animals just won't produce well together. The female doesn't get pregnant or in the case of animals that give birth to litters they have very small litters while if you breed those animals to any other animal rate of pregnancy and litter size is just fine. It's even more common that stillborns and other problems are the result of 2 animals just not combining well. We had a mare that produced wonderful foals and never missed. We had a stallion that bred mares without fail and also produced wonderful foals. Together they failed to produce a foal the first year, after multiple months of trying produced 2 stillborns the next 2 years, and the 4th year the foal died after 2 days from a suspected heart problem. Bred out to any other horse they produced fine foals but together it was a disaster. We sold the mare and she went on to be a great broodmare in someone else's herd with a different stallion.
That's why you always test breed out to another male if you have one when a female is having repeated problems. It proves whether the problem is actually the female or the pair which could warn of other potential problems with your lines and combining them.