Basically if your substrate goes rotten it will produce hydrogen sulfide (poison) then if you or fish ect.. disturb the substrate the hydrogen is released thus killing or stressing animals. So if you observe the lower layers of the substrate turning black or black spots even graying is an indication of hydrogen sulfide being produced. If you do witness this start with boosting flow in the lower areas of the tank this will force the dissolved oxygen into the sand bed, which help if not fixes the problem.
You may see spots in the pic above but that is algae, my tank receives some natural sunlight which causes growth on the front lower glass. One more thing along with black spots gas bubbles may be visible.