I had a similar problem just recently. I ended up losing the whole clutch of eggs. What I think happened with me is that my hovabator is about 5 years old, and for 9 months of the year, my incubator is sitting in my basement. I usually just plug it in and put the eggs in (with moist vermiculite of course). But this last time I got lots of mold. I think that the mold from the basement is equilibrating with the inside of the incubator. So, i bleached it and rinsed it well. Maybe my vermiculite is loaded with mold spores too.
But if your eggs are yellowish and collapseing, it might just be that they are not fertile...in that case...they'll rot in 2-3 days.
-----