First I would do what was just suggested and clip the puppies nails. Long nails can be very uncomfortable for momma. Second, if that doesn't work, DON"T feed the milk replacer you find in stores, make your own. It's higher in fat, and better for the puppies. I have used this recipe many times, and saved many puppies;
10 oz can of goats milk (even better if you can find it fresh)
1 raw egg yolk
1 cup whole yogurt (not fat free, or low fat, has to be whole fat)
1/2 tsp karo syrup
If these are large breed puppies, you can probably go with food mixed with the formula. I don't like to make a special diet for puppies because every time you change their diet they can get a stomach upset. What I do is buy a high quality puppy food, and I put it in a blender and grind it down to a fine powder. I then mix this with the puppy formula. It's better than feeding canned food because it is mostly water. This was they get all the nutrients of the food, and all the calories and protein from the puppy formula. Let me know if you have any questions, I would be happy to help. I have been raising puppies for a long time.