There are several diseases that could cause a caterpillar to turn black and die. One is simply called "Black Death", the scientific name is Pseudomonas Bacteria.
At this point, I would recommend sterilizing a new container and moving them. This disease could still be in your container. You can use that container again, if you sterilize it with a 20% bleach solution. 80% water and 20% bleach. The containers need to be thoroughly rinsed after using bleach--bleach residue can kill them, too.
You should wash your hands with soap and rinse thorough before taking care of caterpillars and afterwards, too. http://faq.gardenweb.com/faq/lists/butt ... 31715.html
Why does a Monarch caterpillar or chrysalis turn black?
"The main way to help prevent either disease is to keep the rearing containers DRY. Warm, moist environments promote the growth and spread of the bacterial and viral 'predators' and cause unclean conditions. "http://faq.gardenweb.com/faq/lists/butt ... 14581.html
Important Info RE OE & Monarchs!http://www.evansonart.com/monarchdisease.html
Several diseases and photographs of those diseases.http://www.mymonarchguide.com/2007/07/d ... spore.htmlhttp://www.learnaboutmonarchs.com/learn ... spore.htmlhttp://www.uga.edu/monarchparasites/whatisOE/index.html
How to tell if butterflies are infected with OE
"An infected pupa may develop dark spots or blotches two or three days before the butterfly emerges. These abnormal dark areas are parasite spores. Spores form on the eyes, antennae, wing veins, but mostly on the abdomen. You can see the spores through the outside layer of the pupa a day or two before pigments that color the butterfly normally darken the pupa. Before a butterfly emerges from the chrysalis, pigments are laid down coloring the scales that cover the butterfly. This normal change in the color of the pupa is symmetrical. The color change of an infected monarch happens earlier and does not create a balanced pattern on the pupa."