Only advice I can offer is to triple check everything in your bator is working fine. Even if it wasn't though, I think it would be hard for the egg to last as long as they did and then go bad. So I'd look for another reason... What was the pairing? Has the mother laid before? Is the father a first timer? Idk this just sounds weird. I have all my eggs in the shoebox from the Container store and I don't poke holes. I also don't open the lid every day to give them air. I have found they get enough as long as there's airflow in the bator.