Setups such as this are notorious for bacterial buildup- debris sinks into the stones and nitrogenous wastes build up, creating a toxic environment. Aquarium gravel can also be ingested by caudates, which can in turn cause intestinal blockages. Do you know what temperatures the salamanders were exposed to? High temps could also have been a contributing factor in their deaths.
For future reference, morphed tiger salamanders should be on a substrate such as cocoa fiber or organic potting soil so they can burrow- in the wild, adult tigers really only enter the water to breed but then return to land to hide in their burrows. Most salamanders also need to stay cool, with temps no higher than the mid to high 60sF.
Hope this information helps. There are excellent care sheets and housing ideas on Caudata Culture that will provide even more info for you.