That's hard. Black spots on vinyl can be several things, but usually none are easy to deal with.
1. Copper can stain black, but usually not a 'spot' -- more of a patchy area. Have you used copper in ANY form, say 4-in-1 tabs?
2. Fungal growth on the UNDERside of the liner, can release some sort of organic colorant. The only real solution is to remove the liner, and treat the surface underneath with an effective fungicide. Usually the liner has to be replaced. High levels of chlorine can lighten, but not remove the patches. Read the Best Guess page linked in my signature.
3. Rarely, black algae will form in a liner pool, if ineffective chlorine levels are sustained over a long period (or if non-chlorine methods are used). Swim down, scrape a spot with a fingernail, come up, smear the goo under the nail on a 3x5 card. Black algae smears dark green.

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