Becky mistook Jon's dramatic behavior to get the stone back as an insult. She assumed that he thought that she was going to pull a supervillian move on him and either rule the world or erase all of existence just for the hell of it. All she wanted to do was have a little fun and get a few nice things in the process. The stone gave her the opportnity to do anything she could think of and since the wishes were infinite in number she could simply unwish any wish that didn't turn out how she expected.(Becky didn't know about the stones limitations.) The sight of seeing Jon make a mad dash for the kitchen like his life depended on it made her upset enough to think that Jon needed to be taught a little lesson. Maybe she could turn him into something like they did in cartoons she thought. The idea of making Jon into a car or a doll or something like that and still being able to see, hear, feel and think sounded like an ideal punishment for Jon. She would simply change him back later that day and then make a plan for sharing the rock with Jon (she had no intention of telling Zoe and Mikey about the stone, she felt that her and Jon should be the only ones in the house to know about it).
Jon desperately ran for the magnetic notepad hanging on the refrigerator so he could write out a message telling her to stop wishing. He only made two steps into the kitchen until he heard "I wish that Jon was..."
