Mother dogs don't have the benefit of prenatal education, and sometimes the maternal instinct is lacking. If your dog has rejected one or more of her newborn puppies, she has a reason. That reason may be biological, instinctive or simply that she doesn't know what to do -- in any case, you should carefully monitor your dog with her newborns for a few days after the delivery.
Problems With Puppy
Your dog's natural instinct tells her that if something is wrong with her puppy, the pup probably won't survive. Mom doesn't know that a human may be able to care for him if he's sick or deformed. If your dog determines that her puppy is not an ideal specimen -- such as if he suffers from a genetic defect, or is sick or undersized -- she may reject him simply as a way of cutting her losses and allowing nature to run its course, giving the other puppies her attention.
Poor Milk Production
Mother dogs aren't always able to produce enough milk, and if yours senses that she can't feed her litter, she may reject some of them. This is why prenatal veterinary care is so critical for your dog. The veterinarian can determine if she is producing an adequate amount of milk to feed her puppies when they are born. If not, you can prepare yourself to feed the pups yourself with store-bought formula.
If your dog suffers from metritis after giving birth, it can cause her an immense amount of discomfort that compels her to reject her young. Metritis is a uterine infection that affects nursing dogs for a variety of reasons, including retaining placenta and/or fetuses. While veterinary treatment can help your dog fight the infection, she may neglect her puppies in the meantime.
Sometimes, mother dogs simply don't know what to do with their puppies. The stress of pregnancy, delivery and caring for puppies may cause a dog to reject her young -- particularly a first-time mother. Similarly, a new mother needs her space after giving birth -- if she feels encroached upon by humans or other pets, she may reject or even kill and eat her puppies.