it might also be your incubator needs a thorough disinfecting. This should be done after every hatch.
If you are sure this is not the cause then here are articles with info on troubleshooting hatching failures/mortality:
http://dlhunicorn.conforums.com/index.cgi?board=identify&action=display&num=1158149341
...there are many articles each having there own unique information to help you figure out where things might have gone wrong such as:
http://edis.ifas.ufl.edu/AA204
(excerpt)
"Troubleshooting: Specific Problems
Sign: Not pipped. Full-term embryo, large yolk sac; yolk sac may not be fully enclosed by abdominal wall, may have residual albumen. Causes:
Inadequate turning, resulting in decreased embryonic membrane development and nutrient absorption.
Humidity too high during incubation or after transfer.
Incubator temperature too low.
Hatcher temperature too high.
Eggs chilled (e.g., at transfer).
Nutritional deficiencies.
Heredity.
Embryological development accident.
Breeder diseases.
Inadequate ventilation.
Prolonged egg storage.
Sign: Pipped. Full-term embryo, dead in shell. Causes:
Low humidity or temperature for a prolonged period.
Low humidity during hatching.
High temperature during hatching.
Nutritional deficiencies.
Breeder diseases.
Poor ventilation.
Inadequate turning during first 12 days.
Injury during transfer.
Prolonged egg storage.
Sign: Shell partially pipped, embryo alive or dead. Causes:
See 8.a-i.
Excessive fumigation during hatching.
Eggs set small end up.
Sign: Chicks hatch early; tendency to be thin and noisy. Causes:
Small eggs.
Differences among breeds.
Incubator temperature too high.
Incubator humidity too low.
Sign: Chicks hatch late. Causes:
Large eggs.
Old breeders.
Eggs stored too long (40 min. increase in incubation time/day of storage, .5% to 1.2% decrease in number hatched/day of storage).
Incubator temperature too low.
Weak embryos.
Inbreeding.
Incubator humidity too high.
Sign: Slow, protracted (drawn-out) hatch. Causes: Mix in the incubator of eggs stored for long and short periods (1.2% loss of hatch/day of storage when all eggs set at the same time; only .5% loss/day when eggs stored for long periods are set earlier to allow a longer incubation period).
Mix of eggs from young and old breeders.
Mix of large and small eggs.
Improper egg handling.
Hot or cold spots in incubator or hatcher.
Incubator or hatcher temperature too high or too low.
Room ventilation system improper; high positive pressure or low negative pressure. Such pressures may alter incubator or hatcher ventilation."