Not sure about the saving part, but whenever i touch my mouse, it switches to KB/M as controls right? Okay, but it will stutter for a moment and the sound drops.
Same happens when i now touch my (normal microsoft xbox one for PC) controller, sound drops for a moment and the game stutters.
It seems to stay smooth as long as i dont switch around like that, but its not normal behaviour.
I think it may also happen when the game auto saves, but i cant be sure on that because it might just be my accidentally bumping into my table or maybe my mouse moves, it happens, so that might be nothing.
But please look into this.