Jon was forced to close his eyes for a moment, and then when he opened them he got a nasty shock.
He was in a girl's room, and then when he looked down at himself, he realized he was the girl!
"Whatthehell?" she muttered, trying to figure out how this happened. "I wish I knew what is going on here."
And then she knew. It is possible for two women to have a child together if the genetic material from one woman's egg is used to fertilize another woman's egg. The resulting child however will always be female, and since Jon wished for there to be a reason for him to be their child, he became female along with his little brother.
Now, so long as his, er, her parents were the same sex (female), he would be stuck as a female as well unless he could figure out a way to re-interpret the wish and be their male child.