It's highly possible that your son did see a worm in the toilet. The human body can be infested by several different types of worms and rather than go into too much detail, I've given you some links that give you lots of information.

http://www.hemorrhoid.net/parasites.php#intro
http://www.herbs2000.com/disorders/worms.htm
http://www.fatfreekitchen.com/home-remedy/worms.html