Whenever we had that issue, we always separated the instigator from the rest of the pack. Usually that solved the issue all the way around for our pups. You'll also notice, over time, that some dogs will produce pups that will kill, gut, eat, etc other littermates whereas other dogs will produce pups that can stay together for what seems an eternity.

Cyrus and Bullet, two former studs we had, would ALWAYS produce litters where pups were regularly killed and eaten if they weren't separated by 8 weeks of age. Neither of those dogs ever produced anything worth keeping. Frosty Paws, the best producing dog I've ever owned, never produced pups that did such a thing. They could generally live together for months on end if I'd let them. So, pay attention to what breeding created that, and keep up with what each individual parent produces bred differently and try to nail it down.