I have them all the time, and it's super annoying. I just use a microfiber cloth to wipe it clean, but it's definitely caused by dust getting into the grooves in the smart cover. Makes me worried that it's grinding dirt in the screen.
I have the leather one. It does the same thing. I was thinking about getting the poly because my 10 y son likes to use the my new toy and got mustard on my expensive leather. I agree that it is over priced.
It's true that lines are left where the spaces are. But overall the smart cover does a surprisingly good job of leaving the screen fingerprint-free. A small trade-off, IMO.
I have the same problem, they started appearing after the first time I put the cover on. A cloth takes care of it, but I don't want to keep wiping it off every time I take it out.
I'm using a Dodocase for every day use now and have a folio case for longer travel