Set a trichlor puck on them for 10 minutes or so. See if they change color, etc.
That looks like rust, like something metallic sat on the bottom and rusted. Any chance you have fertilized around the pool recently with a fert containing iron?
Installing a fence could be culprit. Many times they are not real careful about pieces of metal getting bounced around.
Now try a thin nylon sock with crushed vitamin tablets in it. Set that on the stains. It should either clear the stains or change its color.