There is some sort of blue-colored fish anti-fungal that has been used successfully to keep fungus off eggs. I can't remember the name.
As I recall from our chat, you are raising crested newt eggs. Half of them are genetic duds and will naturally develop fungus. I have never had a problem with this fungus spreading to the good eggs. But if this is the problem, try removing the duds as soon as they are identifiable (by lack of development or by early signs of milky color or fungus).