It looks to me to be nothing more then discoloration. I wipe my M&Ps down with a silicone cloth. Once the silicone is rubbed off or dries up I get similar marking. On mine it is nothing permanent and another wipe down makes it look like brand new.
Two complaints I have against the M&P when I compare it to my Glock is the finish on the slide and the "dots" on my barrel. I have what looks like some sort of a machining rub on the slide that I thought was unique to my gun until I went to the shop and saw another like it. The dots -- while purely cosmetic -- do give the appearance of a poor finish when put together with the slide mark.
All that aside, the gun should still be a keeper as long as it continues to function as expected. After a lot of thought I'm sticking to my G19 as my carry gun but I'll probably throw my M&P in my glove-box on the days that I'm not carrying (I can't carry into work). I've heard that the cheapo Glock holsters that fit the G20/21 models fit the M&P9 well...
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