The stone looked exactly like Jon's, but it wasn't. This stone didn't grant wishes at all, because this stone was just an everyday normal rock.
Fortunately for Jon, he made a wish with the wishing stone before he showed it to Karyn. The wish was to know whenever the stone was used, just in case someone stole it. He could figure out who, then track them down and get the stone back. He was hoping he'd never have to do that, but now it seemed like he would.
The intruder crept back out of his bedroom, leaving Jon to sleep through the night.