* Multiple Fathers: If a female dog mates with two different males within a short time frame, she can become pregnant with puppies from both males. It's even possible for a single litter to have puppies with different fathers.
* Determining Fatherhood: Unless you're doing DNA testing, you can't definitively say which male is the father of each puppy. Even then, it might not be clear if the mating happened very close together.
So, the answer is: You need more information to know for sure who the father is. It could be one of the males, both of them, or even neither if she was pregnant from a previous mating.