Mastitis
Mastitis is a bacterial infection that will affect one or more milk producing glands. This is a painful condition that will cause the female dog to not want her puppies to nurse and she may even snap or bite at puppies that try to nurse on the affected teat. Mastitis can also cause the puppies to become sick if they nurse on an affected teat.
Uterine Infection
There are some instances when the female may develop a uterine infection from either a retained placenta or there was a puppy that died in utero. When your female dog is suffering from an infection, they may harm their puppies simply because they do not feel well.
Sick Puppies
Natural instincts will kick in when a puppy is sick and will not survive. The female dog will push the sick puppy away from the healthy puppies and sometimes they may even harm or kill the puppy to stop its suffering. If you notice there are one or two puppies that your female is pushing away, chances are that the puppy or puppies are sick and will not survive.
Accidental Harming
Some female dogs will accidentally harm their puppies because they are either lazy or careless. Large breed dogs will sometimes lie on puppies, smothering or crushing them. If your female does not have the natural instinct to nose their puppies into the center of the whelping box before lying down, you will have to closely monitor the puppies when your female is moving around the whelping box.
Stress
Some female dogs require a quiet, secluded place to whelp and raise their puppies. If your female is feeling stressed or threatened by too much noise or activity around her puppies she may begin harming the puppies as a way to protect them from any perceived outside threat.
Unstable or Inexperienced
Some female dogs just simply were not cut out to be mothers. These dogs will avoid their puppies, pace and even snap at the puppies if they get too close to her. Dogs should never be bred on their first heat cycle; they are too young to handle the stress of carrying a litter or even raising them for six to eight weeks. Inexperienced mothers will many times not bond with their puppies and will be disinterested in them.
Lack of Recognition
There may be times when new mothers do not recognize their puppies as theirs. Female dogs that have been through a cesarean section are especially at risk of not recognizing their puppies. They will not have formed a bond and may try to harm the puppies instead of nurture them.