It is possible for a female dog to carry puppies that were sired by more than one male dog. Puppies can have more than 2 fathers for the same litter.
Answer provided by Bonnie V. Beaver, DVM of AMERICAN VETERINARY MEDICAL ASSOCIATION. See more of her answers to questions on subjects of animal behavior on http://exchanges.webmd.com/pet-health-exchange/groupstory/13552257.