As soon as Jon made the wish, both babies began to age. They rapidly grew taller and their features older, hair growing on each one's head. When they reached toddler age, Karyn and Jon noticed they were wearing clothes, which subtly changed as they got older. The girl grew into a teenager who was easily recognizeable as Emily very soon, since Jon and Karyn had known her as kids and knew what she looked like as a kid.
Of course, it was unlikely that two random people could have the exact genes necessary to produce Emily again. However, Jon and Karyn had genes that were pretty close, and when the stone had made Jon pregnant it had also changed her and Karyn very slightly so that it became possible for Emily to be theirs.
The boy looked something like Jon, Karyn, and Emily, though he looked the most like the old male Jon. If you accounted for magical aging, it was very easy to believe he was Emily's brother, and that Jon was his mother and Karyn his father.
Finally, both he and Emily stopped aging when they were teenagers--that age wasn't adult, but it was enough to talk like an adult.
"Whew," said Emily. "That was bad. I'm glad you fixed it, anyway... Here, let me have the rock."
Karyn gave Emily the rock. Emily was about to wish their previous life back, when the new boy spoke up and said...