Once you deal with lots of eggs, the probability of you finding problems with a few of them rises, not all hatchlings will be 100% healthy, some do not make it. Every breeder has seen this, it's sad, but it does happen.
In regards to the mold, I'm guessing that your incubation medium is too wet. What is your incubation medium? I find vermiculite to be the best option, just squeeze out the excess water until no more drips out, and fill the container 3/4 full of it.
How many females do you have laying for you?
I ask because I had this one female last year, that threw me out 12 eggs, and all but ONE molded over, due to the babies inside not fully forming, so her days of egg laying are over. So it might be a problem with one of your females...but I think the problem is with your incubation medium being too wet.
Hope this helped answer some of your questions.
Best of luck with future eggs

-Sam