Jon poured himself some cereal and milk, ate, and then said "I wish I knew why my wish didn't work right." The stone glowed, but Jon didn't receive any knowledge, unlike what he expected. What he didn't know was that the stone he had now was the Inverted Stone. It granted the opposite of what he wished for. So, in this case, it would have been as if he wished that he didn't know why the wish didn't work.
So, to sum it up, the wish was granted, but nothing happened, since he already didn't know what was going on.
The fact that his wish seemingly wasn't granted, Jon wondered what might be wrong with it. He picked it up and actually looked at it this time.
"Hey, this isn't my stone. What happened to my stone?"
