Jon typed in "Girl Jon" and fired up the machine.
The machine gave Jon what he asked for and didn't try to twist it.
Jon wouldn't mean for "girl Jon" to be "Jon with a vagina", so that isn't what happened. Instead, what grew in the machine was a naked person who looked mostly like Jon except for everything necessary to being female--not just the vagina, but she had breasts, shapely legs, long hair (which isn't really female but which is what Jon had intended), a womanly face and shape, etc. A normal-looking girl Jon.
The liquid drained and the machine opened. The girl in the machine coughed and said "How did I get in here? I was just outside starting up the machine! Wait, I'm a girl! What happened to me?"
From outside, Jon's mother yelled "How's that build-a-man kit working? I can't believe your grandfather sent you something so science-fictionish."