This may be a sign your puppy isn't processing or getting enough nutrition. Consult with your vet to rule out this possibility before considering the following:
Is this an indoor or outdoor situation? Dogs by instinct will prefer not to poop where they eat or sleep. Maybe your puppy is trying to clean it's environment. ? If it's an indoor situation then it may clear up when you house break your puppy. The poop will be outside the dog will be inside and therefor the dog cannot eat it's own excrement. You can also aid in this process by Learning how long it takes between when the puppy eats and when it has to poop. Make sure that you take the puppy out during this window of opportunity.