Brown Dust on top of substrate

More than likely it's just that...dust! You're always gonna have some sediment on top of your larger sediment (if that makes sense). No way really to get around it, but after you get some surface crawlers like hermits and the like it get mashed down there. You could stick your hand way into the middle to lower levels of the sand and scoop that up over and on top of the dust. That should help.

If it's a new tank, it could be diatoms. Very common in newer setups, usually wears out in a few weeks. Touch the dust--if it's soft and a bit slimy, it's probably diatoms.