Contrary to what a lot of people believe, all mothers animal OR human do not make GOOD mothers. Sometimes a mother dog will "push away" a pup if she knows something is wrong with it and she will not let it nurse. Some mother dogs will simply sit on or lay on their pups and smother them. I have even heard of some mother dogs and cats that will "eat" their babies. These are animals that should not be allowed to breed again since you may get the same results. If there are any puppies left, I would strongly recommend to you to take the pups away from the mother immediately and prepare yourself to bottle feed these pups until you can get them weened. Your mother dog is not being a good mother and should not be allowed to breed anymore. I'm sorry you have had this bad experience, but maybe you can save the other pups if any are left.
It could be that she was stresses while giving birth. Normally a dog wont harm her pups, but sometimes when the environment is unusual or disturbing, the mother might kill or even eat her puppies.
Your supposed to take the pups away from her 4 a while. =[ poor pups