Hi Kristy
Without being able to examine your son I cannot be 100% sure but one possibility is:-
Inside your son’s body is a ligament that attaches to the penis. If this ligament is short or is connected a little closer to the end of the penis than it ought to be it would cause the problem that your son has. This ligament is not really needed and it is a relatively easy operation to cut it and thus lengthening the penis.