Hi Trae;
I can think of two other possible causes:
1. Copper oxide. Could be from a pool heater, or from a copper algaecide. Test by placing or holding a Vitamin C tablet against the spot for 5 minutes. If it lightens or disappears, it's copper.
2. Fungus from under the liner. Sometimes fungal colonies will develop under the liner. This usually happens when the ground is very wet and warm. There's no real test, except the color is IN the liner, rather than ON the liner. Unfortunately, there's no fix, either, since the source of the stain is fungal pigments bleeding through the liner from the dirt side.
If this is the problem, there are antifungal treatments you can do to the dirt / sand / vermiculite the next time you replace the liner.
By the way, if it's fungus, it usually will NOT be against the pool wall, but against the dirt / sand / etc.
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