@julihy, please don't blame yourself. I doubt that you could have done anything to help them.
And the sow did NOT hate the pups. That's a ridiculous idea. It also had nothing to do with the fact that she chews on things. It had nothing to do with malnutrition, or the fact that she was a single sow. @
peanny77, do NOT post misinformation. We take very seriously our responsibility to provide accurate information, and posting things like this are not accurate. You are a relatively new owner yourself, so please refrain from publishing things that do not come from reputable sources. If you continue to do so, you will be place on moderated status so that your posts have to be approved by a moderator.
Guinea pigs very rarely do anything harmful to pups, even if they are stillborn. To me, the most likely explanation is that the pus were still enclosed in the sac, and that they were bitten as the sow was trying to eat the sac.
I'm very sorry the pups were lost. I hope you can find a buddy for your pig quickly.