We had this happen with a dog at the kennel. Killed all puppies in the litter except for one.
What I understood was that she did it because she felt threatened. Normally we removed the pregnant bitches into a separate room days prior to their whelping... she gave birth early and unexpectedly (I was not working there at this point so I don't know what the exact circumstances were), surrounded by a dozen other dogs (all in their own runs, but still) in a very stressful environment. It's a fight-or-flight type situation, and if she's stressed she'd rather kill the puppies and be able to run/etc than risk the lives of everyone involved. I'm curious what the validity behind that is.