What are these spots?

I would suspect that it's black algae.

Black algae is a type of bacteria called cyanobacteria. Cyan means blue-green.

See if you can scrap some for examination. Black algae is a dark green spongy bacteria. Don't scrape with anything that could damage the liner.

The bacteria can be toxic, so be careful. I don't think that it's crazy dangerous, but be careful anyway.
 
Is that a tree in the refection?

I agree it is probably black algae but I have Privet tree that produces little purple berries and when they make it to the pool bottom they leave dark purple stains for a few days.
 
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