In my experience... if your eggs are heavily soiled you get more early deaths. So keep your nest boxes full of nice clean bedding material. It is true it is best to NOT wash hatching eggs as it washes away the protective bloom, but better to wash a very soiled egg in hot water than to set it and lose it from bacteria, or worse lose it to bacteria and have it explode all over your incubator.
As long as an egg doesn't go completely rotten and explode IN the incubator your other eggs should be fine even if one is a dud. You can usually take a whiff as you open the incubator and tell if there's a bad one in there, then sniff one egg at a time until you find it. Sometimes they start having crusty bubbles seep through the shell and are easy to spot. Also if you will candle at 10 days and remove the clear ones they will not be suspected stink bombs later.
From my research a lot of late quitters are caused by one of two things- too much temperature fluctuation during incubation (make sure your incubator is away from windows, exterior walls, and drafts) and vitamin deficiencies in the parent stock. I know one time I bought two dozen hatching eggs, about 20 made it to lockdown, but only ONE hatched. I'm assuming the seller had deficiency problems in the flocks because everything went exactly right during the incubation, and my other eggs in the same batch had great hatch rates. Some people feel that it is better to pen your flock and control their diet exactly for breeding purposes than to free range them and chance they are missing something in their diet. Humidity CAN also be a cause, but if your temperature is steady even humidity swings should be tolerable. One last possibility is that your stock is too closely related- too much inbreeding can cause fertility and hatching problems- but it would require multiple generations of sibling matings, etc.
This is based on my limited experience and some basic internet research. Hope it helps you!