The “wrinkle” here is the setting of the putter on the green. Unless it was witnessed it will be tough to decide if the action affected the ball and caused it to move.
But barring the person causing it to move, (if say a gust of wind had clearly caused the movement) the concession applies to the NEXT stroke. Since the ball had not been marked and replaced, and had that wind caused it to go in, the score would be 3 for the hole and the concession is irrelevant.