Certainly you can have dust and other "yuck" in the mirror box. A blower can get rid of most of that. If the specks don't show on your images, they're just on your focus screen or maybe the mirror. The grainy texture from the matte finish will show up more in out-of-focus portions of the field. These do not affect your image. If you find them distracting you can swap focus screens for a different style, but be careful as some need to be shimmed to the proper focus.
I scratched up a focus screen in my K10 trying to swap them. I figured out what I was doing wrong and when I added a split-focus screen I got it right. I didn't bother doing that with the K5 or K3II even though I shoot a lot of macro. I usually find I can hit focus manually with the stock screen and indicator.
---------- Post added 11-02-16 at 08:04 AM ----------
Originally posted by Sterby It is ground glass, it tends to have a pattern but the digital bright screens are much more even than the high contrast ones. It is also possible that someone touched it and left a fingerprint which is super hard to get off properly. Can't really say much without a picture.
I say bring it in to a camera shop and get it checked, if it is fine than the experienced staff can reassure you, if not they can fix it for you.
That is true - skin oil (sebum) can stain like that. Again, it won't affect your image but can be very distracting.