Not sure if this is what you are talking about or not, but I've had (and I've read of at least a few others) a lot of problems w/dust finding its way into the viewfinder - I personally am blaming the crappy eye-cup piece that came w/the camera! It does not have any impact on the image, however, as it is only seen in the viewfinder. Do you see the dust in your actual image (or if you use live view), or is it just when you're looking through the viewfinder?
My problem is more annoying than an actual problem, so I tend to not care too much. I just don't know why they went w/such a piece of crap for the eye-cup, the one on my mark ii is significantly better... oh well!