German Shepherd dog

Check her thyroid level she may be low a common cause for one pup litters. Marlene

I'm of the opinion your issue could be a variety of different things, including some of the suggestions already made. Here are some other things to consider:
1. What is the females' mothers record for litter size? Did they also produce smaller numbers in litters? If so, then your girls may have inherited their mom's disposition for not ovulating many eggs when in heat. Remember, the female always determines how many pups will be born depending on how many eggs she releases when she ovulates, not the male. If he's healthy and has a normal sperm count, the eggs will fertilize if they are present. If you bought females from mothers who produce few pups, then expect your girls to potentially do the same.

2. What type of heartworm meds do you use? I have seen that some heartworm meds can contribute to low birth numbers and even miscarriage in GSDs if given when they are being bred. I had 2 of my own females produce me 1 pup by one and 3 pups by the other on their first breedings while on Heartgard Plus, but when I slacked back on their heartworm meds from the beginning of heat until they whelped, they had litters of 7-9 pups 2nd time after the small litters just fine.

I you decide to try them again, try slacking off the heartworm meds, and you can try a product called Solid Gold Concept-A-Bitch 2wks before they start their next heat when you plan on trying a repeat breeding and see if that helps your girls produce better. If neither of those things I've mentioned seem to be the culprit, then it could be something like thyroid, etc. Best wishes.