Sometimes, it takes a vet pathologist to figure out what kills them. There could have been something that caused an interruption in blood flow to the bowel or to the oviduct, which caused them to appear black. I will tag @casportpony and @azygous who may have seen something similar with one of...
Sorry for your loss. Did you take any pictures of the organs during the necropsy? Did you open her crop or gizzard? Was any of the bowel black or bloody inside? Coccidiosis and enteritis are two illnesses that usually affect young chickens. Could she have eaten something like rat poison or...