i've read about this before as well...
i've got a black leather smart cover, which i love, but boy does it leave lined marks on the glass screen.
it leaves marks on the screen where the 3 long grooves are, which ironically touch the screen the least. the main 4 leather panels dont leave any marks. and it's a quick thing - it doesnt take days to happen, it happens all the time.
and i dont know what they are. these marks are easily removed by a cloth, and aren't black (so not the leather residue), and happen even when the cover is cleaned. its most strange. it isn't a problem, just a minor pain in the ass.