Why are my eggs dimpling?

So my female dropped 8 eggs around the 27th of March*. Since then, I've lost all but three. That's kinda been a bummer, and even though this is my first clutch, I didn't think I'd lose 5 eggs. Anyway, the eggs that are alive right now are looking pretty dimpled and 'wet' in some areas. There's no water dripping onto the eggs, in fact, I've been keeping a lightly moist paper towel over them to keep anything from dripping onto them. My temps are 90f, and my humidity is 100%. What's going on? One of the eggs is starting to smell, but it candles with red, living veins. I'm really hoping that these three make it to full term, but I'm definitely starting to worry.

Definitely weren't dropped in March, hahahah. Losing track of time.
LAST EDIT, I SWEAR. Checked when I posted about the eggs being dropped. Now we're on the right track, lol

I can't be of any help, but I know somebody will ask. Do you have any pics?

What kind of substrate do you have the eggs on? What are they in?

They're on vermiculite in a 6qt tub. My incubator is homemade out of a cooler, I use a Herpstat for temperature control. Unfortunately I can't upload pictures.

How wet is the substrate? With vermiculite, you want it so it clumps when you squeeze a handful of it. But, if water drips out when you squeeze it it's too wet.

Are they directly on the substrate or on a light grate?

The substrate moisture is just right so that when I squeeze it, it just clumps up. The eggs are directly on the substrate, as well.

What are you using to keep the humidity in the egg box with? I use press and seal on mine to keep the humidity in. Some eggs just dimple its just how they are, as long and the tub is sealed to hold in the humidity and your eggs aren't sweating or growing any kind of mold or fungus, candle them and everything should be fine.

Do you have a fan in this incubator? A fan is important to push the air around to make sure there are no hot spots or cold spots inside the incubator Your egg box should be surrounded by warm air that is a constant temperature. If temps are fluctuating too much condensation can build up on the eggs themselves causing them to be too wet.

If there is no water dripping onto the eggs and they look wet in some areas, what sense does it make to have a moist paper towel over them?