I have had a couple of stained areas on my liner, on the side slope in the deep end. I've brushed vigorously, with little effect; it's been there for several weeks. I was about to decide it was metal staining or something bleeding through from the back side. Anyhow, I brought the FC up to shock level, and after a couple of days, the stain is completely gone! I guess it was algae after all and the combination of brushing and chlorine finally killed it off. Still learning.