They don't know anything.
I work at Petco and I'm going to disect this claim.
First off, the ferrets' water comes from their water BOTTLES. Ferrets would just tip their water bowl if we gave them one while they played. Their "water" was actually their dry food mixture. They have glands in their anus and, before they're shipped to us, go through surgery to have these removed. We mix their dry food with warmer water, thus the "dirty water." Softer food equals softer stool so that they don't hurt themselves after surgery.
Second, their litter comes in a variety of colors, depending what product that Petco ended up using that day. It can be a dark brown to black color. As far as the feces being everywhere... these guys have the SHORTEST digestive tracts I've ever seen. They probably poop every other hour. YOU try cleaning up after five of them every hour. My Petco does a spot check in the morning, when we open, mid day, when we close and right before we leave. It helps, but you're NEVER going to keep it spot clean.
I'd like to know how you know they looked "sick." Is this just a ignorant assumption?