I had similar experiences on my M8 (had 40K+ shots); there was common acceptance at that time that this was partly from the shutter (sort of out of the box), residue. And the longer one leaves it there, it gets harder. The M9 is the same mechanism as the M8, so might have the same user experience.
M9 users got a mail warning them not to use wet cleaning (on the original first generation sensor); there was an advise to use a kind of gum stick (like an eraser) that absorbs the dust.
Interestingly, my M240 sensor (12K shots) stays much cleaner: out of the box and during use and is easy to clean.