The marks on the side of the cylinder come from hot gasses swirling around the screw hole in the top strap for the sight assembly on your revolver. The factory screw is not long enough to be flush with the inside of the top strap. The solution is to call S&W and ask for a longer screw! They will send one to you for free.
I went to my local hardware store and bought a screw while waiting for the S&W screw to arrive, and although it sticks up a bit more than the S&W one, I've kept it on my 686.
The first picture shows the cylinder "window" and the bottom of the replacement screw, indicated by the red arrow. The key thing is that the screw is filed down before installing it so that it is exactly flush with the inside of the top strap. This eliminates the small pocket of the screw hole that creates the marks on the sides of the cylinder.
The second picture shows the top strap and sight assembly with my ad hoc replacement screw, which I've gotten used to now. (I am keeping the one S&W sent me for my next revolver).
The third picture just shows my 686-6.