I also have this issue. It's a three fold hit. Sound breaks up, framerate drops and the controls actually lock in the last in the last I put I made.
It's a really strange thing as it seems to have nothing to do with what's going on on-screen. The game runs silky smooth during the most hectic scenes for hours, and the out of nowhere it'll happen. For me, it has gotten worse since the last MGS V patch.