Hmm...assuming the two only tied once, even twice, it would make sense that the number of pups was low. Do they know when it could have happened? Maybe the pups were born too early, which would account for their small size. I really don't know
I can see where the mom and pups would need to be checked, but I wouldn't exactly want to stick my hand in and come back with a nub either!?! I really don't have any advice on dealing with aggressive dogs, no matter how good the reason for their actions, at least not when the dog is your own. (We actually had one put to sleep due to his trying to bite...well, more like due to what was causing him to act that way, but that is a different story all together...)