At this age, they should still be with mom. Good breeders leave the puppies with mom so that she can teach them what they need to know. Most stay with mom for 8 weeks. She will begin to wean them herself around 6 weeks of age.
This could be a contact allergy. I suggest that you wash the feet well with a peroxide or betadine wash and then apply some neosporin ointment to any red or abraded areas after you dry the feet completely.
If this does not help, another visit to the vet will be needed.
Let me know if you still have questions.
