I missed part of this, but it may not be anything you did, it could be the eggs.
Where did you get them, how were they handled, what sort of incubator do you have, and have you double checked your temps and humidity with secondary thermometer/hydrostat?
There's also the fact the some eggs just quit, and there is nothing you did to cause it. If most of your hatch is OK, and its just a few eggs, no worries. If you lose the entire clutch halfway through, then you have problems.
I got them from a local breeder pick up. They were on her porch in 40 degree weather for about an hour. I have the brinsea mini II advance and I've been checking my temps with a thermometer/hygrometer I bought. I calibrated the hygrometer. The humidity went up to 53% once near the beginning of the hatch, but the rest of the time has been staying between 35%-45%. The temp went to 100.0 one day for no reason last week which is during the time I lost these developers. Would that have done it? I had 8 eggs, two were infertile, and out of the 6 two/three stopped developing.

I put in the automatic turner now, do the point end of the eggs face the inside or the large end?