The chamber may be cut too deep or the ammo cases you are using may be on the short side. 1) are you using reloads? if so what is the case length? 2) What does the dimple in the primer look like?

I field stripped my M&P9 and a loaded round sticks out of the chamber just a tiny bit farther than the lugs, but several empty cases would go in farther than the the lugs. This leads me to believe that the bullet engages the lands of the rifling before the case mouth engages the end of the chamber.

My M&P9 does not have the marks you showed, I probably have 150 rounds through it.