I have this problem in my pebble tech pool. If you have a over flow valve plug it and fill your pool water level to the dark stain and make sure your chemical levals are good. Run your pool system...
I have found that building the acidity up a little high for a while often fixes that problem. Stains are often the result of tannin from some sort of vegetation on the bottom of the pool. Additional...
Add stain and scale remover to your water. I will get those kinds of stains too if I don't use the stain and scale when filling the pool, or a couple of times after big big rains.It is caused by...
If the stain isn't too big you can try putting some dry acid or chlorine in a sock and laying it directly on the stain leave it there for a while and with a bit of luck it will get rid of it.