Question: Stewie asking "How'd you get all those cuts on your butt?" Is this a joke/reference that went over my head?
Answer: He might've been on the show "Stabbed in the Butt", which was in a Family Guy cutaway.
Answer: Old people tend to be wrinkly. Stewie is a baby who doesn't understand that.
Answer: Old people usually have poorly maintained butts for some reason. I work at a hospital, and it's the first place they check for sores.