I don't think one dead crab would cause any problems like that. Doing a water change with tap water would have more of an effect than that. Did you treat the water with any dechlorinator? The brown on the bio-bail sounds likes it's just algae. I don't really know what a bio-bail is but it sounds like it's the perfect place for algae to breed. And as you said there has been an obreak of algae in the tank, so of course there is going to be algae on the bio-bail.