The tiny black flies you are seeing are Phorid or Hunchback Carrion Flys.
They are a serious problem in an incubator. Dead eggs will attract adults, and the maggots are capable of burrowing into and killing heathy eggs. The maggots will also kill pipped hatchlings still in the eggs, and also can burrow into the unhealed umbilicus of newly emerged hatchings. Nasty things! You'll need to wage an all out war on these!
First off, you'll need to keep the snake cages meticulously clean. Be sure to remove all fecal matter within a day. Either flush it, or pour rubbing alcohol on the feces when in a trashcan.
As for incubating eggs: You'll need to remove the clutch of eggs from the incubator carefully cut away any dead eggs or slugs. Then wash the the remaining eggs gently under 80-84 degree (use a therometer!) running water. Use a soft bristle brush to remove any eggs/debris from between the eggs.
Once clean, change out your incubation media with a fresh batch, reset the eggs, then put the whole incubator box inside a snake bag or pillowcase (this will keep the flys from reinfesting the clutch.) then set this inside your incubator.
Every day or two, open the box and look for flys or maggots on the eggs. If any are found, repeat the steps above. Keep the pillowcase over the clutch until well past emergence (once the umbilicus is closed). After the clutch has hatched you can treat the room with VAPONA.
NOTE: Do not follow the next steps of you have either Asian Ratsnakes or fishtanks in the same room! I have BOTH, several dozen VERY expensive catfishes and a group of Taiwan Beauty Ratsnakes that I've had for over 12 years! Makes it a bit tough for me to fight these little buggers.
From there, remove the water dishes from your adult snakes and hang a "No Pest" Strip (Vapona) in the room with your animals for a week. Give the snakes a week to rehydrate, then repeat the procedure.
Good luck with the fight...
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Later,
Paul E. Turley