I had a similar problem with a clutch of corn snake eggs last year. Shortly after the eggs began pipping, I noticed there were tiny larvae of some sort crawling around the eggs' slits. They did look like tiny fly maggots. I didn't do anything except brush away what I saw and removed eggs as soon as the babies left them because the larvae/worms/whatever they were were quick to enter the shells and feed on whatever goo was left behind in there. It was a nasty experience but thankfully none of the corns were lost and I haven't had that problem since.

I'm sorry some of your babies didn't make it.