The stone he put in its place looked exactly like Jon's stone, except that it wasn't. It was the Spelling Stone. It worked just like the normal stone, except that before it granted someone's wish, it changed one letter of it, thus changing the entire meaning of the wish. (The words "I wish" are not affected by this.)
For example, if Jon said "I wish I had a new car," then the stone may grant the wish as if he had said "I wish I had a new jar," or maybe "I wish I had a new war," or maybe even "I wish I had a new cat." Just as long as one letter was different.
One letter can change everything.