I think most late stage deaths are caused by not enough humidity. The chick needs maximum moisture, to be able to wiggle around inside and unzip it's way out.
This sounds like it was responsible for the problem. If you know eggs are going to be hatching soon, about 3 days beforehand you should be locking down the incubator and not opening it at all. Add extra water before this, so that your humidity is in the 65-70% range for hatch.