Crowded conditions can cause problems. In my Glad containers which are 13 cups, I've been raising 4-6 caterpillars. The larger 4th-5th instars that I bring in, I've been raising those in separate cups.
Many people have been having problems and I think some of it is (nuclear polyhedrosis virus) NVP and Nosema. A chrysalis that gets dark could also be OE.
Best thing to do is get rid of the sick caterpillars/pupae, bleach, rinse thoroughly and start over. If you have caterpillars that are not acting sick, then put them into a separate, sterilized container and don't over crowd. I know its hard not to take in every caterpillar, but you can't raise them all. I've got caterpillars outside and I've got caterpillars inside.
Herndon, VA (USA)
Take care of the small things....