It also might just be dirt/dust that gets stirred up when you vacuum and then settles back down to the floor. That often is the case in my pool. The installer used tape to tape together the pieces of foam under my liner. When you are looking at the pool liner, you can't really see it but it caused slight "ruts" and the dirt likes to settle into those ruts along the liner floor of my pool. I can vacuum one day and then the next day, the brown "lines" are back.