Rocks or pebbles, on a substrate aren't meant to look or be clean. Substrate is however a great place for beneficial bacteria to grow, which helps water quality itself.
Many people think the substrate must always Look like it came straight out of the bag when its been in water for a while, I have never seen a dirty substrate in my life (unless, someone threw some junk in there unnecessarily or something.) its just apart of the bio diversity in your pond, substrate is also a good place for micro organisms such as Cylops's to live as well as copepods.
"muck" as a previous member stated, is just usually regular fish feces, and waste building up. Other organisms live off this and is again, part of the bio diversity in your pond. You can plant plants in that substrate With the muck as nutrients such as Sagitaria sp. to form a pretty carpet plant in your pond. It also again, helps water quality improve. I strive to have a mulm in my substrate.
Hope this helped
@Nyboy
Nate