What you are seeing could well be smears and hard to remove stuff. I have the high res. 27" and have yet to find a way to keep it totally clean. I have been using anti-static cloths slightly damp, as recommended by Apple, but the coating "Drags" and it's impossible to get all the stuff off.
I don't know where it comes from, as mine has never had a finger laid on it except maybe when moved on to my new desk.
I have it covered when not in use too.