Hi, sadly this is a subject I came to know a lot about
Basically, if some of your substrate doesn't get enough oxygenated water to it, the beneficial bacteria die off and are replaced by nasty, anaerobic (oxygen-hating) bacteria that produce sulphur dioxide as a waste product. The sulphur dioxide forms a gas pocket which when disturbed by a bottom feeding fish, for instance, dissolves into the water instantly as sulphuric acid and... goodbye fish
Dead spots generally form under rocks, tank ornaments or bogwood, which is why you should move them around every once a while and clean underneath them. If you ever smell a smell of rotten eggs in your tank you need to react immediately to clean up the problem before your fish die - I lost quite a few fish when this happened to me.
The problem is that once you have sulphur dioxide gas bubbles and sulphuric acid in your tank, it will harm your fish before you have much time to do anything about it. 100% water change and paranoia for weeks afterwards is the only way I know to fix it. In the end, I swapped out my entire gravel and had a bit of a hairy time putting my tank through a mini-cycle (this is not fun when you've got rummynosed tetras and pencilfish). Since then I've always told people who inheirit and old tank to do a total strip down if at all possible, whilst keeping the filter and some of the top gravel to avoid the tank having to cycle all over again.
Anyway, prevention is better than cure so make sure you give your gravel a periodic sort-through to aerate it and don't have it too deep. Plant roots, once established, will help keep the substrate aerated.