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Hi, the picture looks to me like early stages of dry rot. It always happens above the water line. It takes many years before any serious damage will be done. Eventually the liner will become dry and brittle and start to fall apart. Many years down the road. The only cure is to keep the sun off it.
Later, Dennis
I can only add this:
When you say "I just opened my pool" do you mean after it being winterized and closed for the season? If it happened during the course of a a whole "winter" (or whatever the off season is in your area), it could be a lot of things. Just about anything could have slid down the pool walls at those locations and caused it. Liquid fertilizers being used on your lawn by a contractor, some one sealing your wooden deck with a chemical product, acid rain. Did anything like that occur in the area of the pool while it was closed?