I am also a fellow Apple smart cover user in Singapore! I bought my dark grey smart cover on 31 March 2012 and just one month into using it, the brown marks started to appear. Initially I didn't dwell too much into it but a few days ago, I found out that more spots surfaced and the stains rubbed onto my iPad as well!
Did a quick search online and chanced upon this discussion thread that the brown marks are apparently rust and some users are unable to remove the marks on their ipad. I already called Singapore's Apple support and they told me there is nothing they can do about it as they have not heard about this issue before and they told me to approach the shop i got it from.
Hence I went to The shop (a rather well known and famous IT retailer) and well they basically said they can't do anything as they are only a reseller. What the guy did was to try and wipe off the stains on my smart cover magnetic strip. He used the same cleaner as what they will use to wipe the screens. He said its primarily due to dust trapped in the gap and was rather sarcastic by saying "nobody actually buys the smart cover because a lot of people already complained on forum." Oh well, he suggested me going to the apple service centre instead. The only helpful thing he did was to search for the addresses online and printed a copy out for me.
Looking at the response here, I doubt going to the apple service support centres in Singapore would help.
The lighter stains can be removed but most of the stains were still around. This doesn't solve the problem I feel cos 1 month down the road, newer stains will most probably surface again. I don't mind wiping the stains off here and there but the stains may just get rubbed onto the iPad itself and if one does not discover early, might not be so lucky to be able to wipe it off easily.
Dos anyone from Apple read this forum? Can someone from Apple provide a good explanation on this and give a solution? Thank you.