It was an anaerobic area in the substrate where no water movement had caused it to turn...well anaerobic. If you smelled it, it probably would have smelled like rotten eggs/sulfur. Over time, if the substrate becomes like that all over, it will release the stinky gases as bubbles up through the water, which is noxious to the fish.
Stirring the gravel every so often will prevent this from happening (because it allows air/water movement in there. If you find a dark spot like that again, you can just till it up to the surface. Come back the next day and it should be regular sand-colored sand again
It happens more with sand and smaller particle substrates because they compact more. I've experienced it in a sand tank, too.
"http://www.aquarticles.com/articles/plants/kumar_substrate.html"
A small blurb in there under "Substrate Particle size" says basically what I just said.