Black stains like that often result from shocking pools that have high levels of copper. Algicides,Nature2, ionizers, eroding pool heaters are all possible sources.
Using HEDP + low pH (~7.0) + low chlorine + brushing can sometimes lift the stains. Using polyquat while the chlorine is low can both protect against algae and help filter any metal particles that form. The HEDP breaks down over time; as it breaks down and the chlorine rises, using skimmer tabs when re-chlorinating can help deposit the copper on the filter, instead of the pool.
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