One in 10.000 chance that a newgen coming into your club through youth intake will be your son. So it's highly unlikely. Even reloading the game, from the day before the intake, over and over again, it would take ages to get a son.
One time I did it manually, by having the in-game editor enabled. Changed his name, and put me as favored personel due to "father". So it can be done.
From the handheld version i know you need to have a player that you bought play a minimum of one match for 10 consecutive seasons and retire at the same club, not sure if that's the case with the PC version. I just used an ingame editor to fast track it by creating a son by editing a random player (PC).