The stone he put in its place looked exactly like Jon's stone, except that it wasn't. It was the Extra Stone. It worked just like the normal stone, except that it always made an extra change to reality after a wish was granted that had nothing to do with the wish.
So, for example, if Jon wished for a pizza, then he would get his pizza, but reality would also change so that his mother becomes a man, or Jon becomes ten years old, or everyone in town becomes a shemale.
Anyone who heard the wish would notice all the changes in reality.