One common cause of pool staining is metals. Metals are sometimes found in our water supply but are often ingredients in chemicals used to kill algae. In low doses, these chemicals are highly effective in destroying algae, but in high doses, they have a tendency to cause staining on plaster, vinyl and fiberglass. The best recourse to combat these stains is to use a product that is 100% ascorbic acid (basically vitamin C). Before going out and buying a bottle of ascorbic acid, take a vitamin C tablet and drop it on the stain. If the stain is gone when the tablet dissolves then you know that ascorbic acid will work. If not, well, you may be a candidate for an acid wash (don’t try an acid wash yourself, it can be a very dangerous process). While you’re at your local pool store, have them check your water for metals and purchase a metal remover to get the metals out of the water once they have been “lifted” from the surface of you pool.
One note: If you are using chlorine tablets from a “big box” store that has blue specks in them, stop. The blue specks are metals that are most likely the cause of your staining. Use only tablets from a pool supply store and you should be fine. Proper water chemistry, without the use of metals, can prevent algae. Use metal-based algaecides only when absolutely necessary.