Big Problem With My Eggs

Eeeewwww....
Sorry... The thought is icky.
But that's aweful this is happening so early in incubation.
It's a bit more risky.
Hope everything works out and you get your little dudes out with no harm and good health.

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if it helps the flys that seem to be laying them look like little fruit fly things

just clean the flies/mags frequently, in the future if you have an egg go bad, either leave it be, or cut away bad egg, leaving just the pieces of shell attached to the good egg(s).

I had a fly prob also, but now there are a few spiders in my snake room, my sigoth always tries to remove them (he hates spiders).

It depends on what type. I'm assuming the ones in your house would be like that..
but there are types that feed on living animals that will let them.
I've had rescue newborn kittens that were healthy EXCEPT they were covered in fly larva and the larva entered the ears (that weren't even open yet) and anus,etc. I think these are bots though and not something you'd encounter indoors.