I have the same problem. Felt like there were bits of metal coming through from the backside of the long plastic strip on the cover where the magnets are. If you press down and rub where the stains are you could feel something behind the plastic, some bits of metal had protruded and started to scratch the ipad. Went to the north Georgia Apple store yesterday and was told it was normal wear and tear and the solution was to purchase a new Smart Cover with the built in back that doesn't use magnets (at full price). I was still under warranty. I bought a replacement, the hassle of arguing was not worth the money.
The scratches on the ipad don't bother me, small enough to chock up to normal wear and tear, scratches would happen inevitably. Had scratches on my iphone as well, new out of the box, but they didnt bother me, would have scratched it myself eventually anyway. However the cover seemed like a defect because metal was coming through the plastic from the backside and continued use would mean more damage. If it had been that the plastic strip just worn thin and the aluminum on the hinge made contact with the ipad I would not have even tried to get a replacement , I can understand that to be normal wear like your shoes wearing thin. Bottom line is the customer service seems to be hit or miss, no better or worse than other brands, I've had two experiences with Apple customer service, the first was good.
I had been leaning towards switching to a Mac, always had been a windows user and my pc is slowing. I can accept the non serviceable nature of a Mac if the customer service is excellent and they stand behind things that are clearly not the customers fault, I'll stand behind things that are my fault. However this experience has led me to conclude that I need to stick with windows, at least then if my hard drive crashes or processor goes bad, I can drive down to my local microcenter or tigerdirect and buy the part and replace it myself for a 50~100 bucks instead of making an appointment, and spending 1.5 hours at the Apple store for a 50/50 chance that they'll either stand behind their product or direct me to leave it with them for a repair cost of several hundred dollars. Not to mention the upfront cost of the mac is twice the cost of a comparable PC.
