If this change occurred within a day or so of pupating, I believe the typical cause is NVP (nuclear polyhedrosis virus). The chrysalis will leak black fluid all over on it's own or when you try to take it down. it's always a messy process. This happens usually with cats that have black blotches. I isolate them as soon as I spot them. Most of the time they don't survive and turn brown and die before pupating, but some do, and when they do, the chrysalis soon end up looking like the one in your photo.
Last year we had a 3rd instar cat with light brown patch on one "shoulder". The brown patch turned into black as it matured, but it pupated and a butterfly eclosed that was perfect in every way except that one of his forewings was malformed. I may be wrong, but I suspect an injury -- it developed the brown patch after it had somehow lost an antenna and I always thought a larger cat had nibbled on it. Incidentally, he had two perfect antennae when he eclosed....

If the cat was apparently unmarked, sometimes the brown internal fluid signals tachnid maggot emergence in the near future. I had ones like those on the hammock frame outside...
