It seemed like a safe wish, now that Jon had discovered that he could retroactively add time limits to wishes.
But he still hadn't thought it through. As soon as Jon made the wish, he had prepared to walk around, maybe talk to his transformed dad. But instead he suddenly was wearing different clothes and his room was different. And his body felt different. Taking stock of his situation, he realized that first of all, the transformation had affected himself too and he was female from the waist down, and second, not only was he wearing different clothes and his room was different, it wasn't even the same house.
Jon walked over to a mirror and looked at himself. He looked somewhat like himself, but somewhat not, even though transforming the lower half of his body shouldn't transform his face. He also looked maybe two years younger.
Then he finally figured out what had happened. Wishes change reality. If he changes his dad so that he is partly female, his dad and his mom couldn't have had children any more. Instead his dad must have had children with someone else. The house he was in must be the house belonging to his dad and his dad's new husband. Wishing to change his dad had changed his own parentage too--his dad gave birth to him, and his new dad was--who?
Since he was also younger--maybe 15 instead of 17--that meant that his dad had married someone who already had children his age from a previous marriage. The timeline wouldn't work if Jon had stayed the same age as before (barring affairs) so Jon had become younger, allowing him to be born without affecting the other child.
But whose father had his dad married? (He assumed it was a marriage, though of course they could have just been living together.)