Skimmers tend to pick up iron stains. If it's INSIDE the skimmer, I wouldn't worry about it (unless you are an obsessive neat-freak, and can't stop )

Either way, if you want to test that, get some vitamin C tabs, wet them, and hold them against the stained area for a few minutes. If it's iron, you'll see some lightened areas. If so, we can tell you how to remove the iron.