Liner Stain

Try rubbing with a regular kitchen scrub pad. If needed, use a little mixture of chlorine and water. Do a test area first and be careful to ensure you don't scrub too hard or remove any coloring. If that does't work, try a Magic Eraser in a a test spot.
 
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It looks like UV damage and not something from the water because the skimmer faceplate is clean and that would have the same stain if it was from the water.

Vinyl degrades in UV and you can see this on PVC in places like Tucson AZ where they get extreme UV.

The PVC turns brown.

This is why some places require the PVC to be painted.

CPVC, PVC Pipes, and Ultraviolet Radiation

UV light radiation can cause portions of the outer shell of CPVC and PVC pipes to degrade slightly, but not significantly. Pipes that are exposed to sunlight will slowly begin to have a visible variation, called “UV Discoloration”. Depending on the pipes’ color, it can start to have a brownish or yellowish tint. When exposed to direct sunlight, CPVC and PVC shows “UV degradation”, but only between 0.001 to 0.003 inches. Once pipes are removed from the direct exposure, the ultraviolet rays no longer affect them.


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