Most likely your son has a fissure (small tear in the skin) near his anus, which would be nothing to worry about. Did his doctor examine him when you took in the stool sample? If your son is acting fine and has no other symptoms, I think it is safe to not take him back for another check unless pain, diarrhea, or another symptom develops. If you think your son might be a little constipated (which can cause tiny skin tears when he passes a BM), then try asking him to eat more fruits and vegetables (maybe easier said than done, I realize).
Yes, if the doctor did not find a small skin tear, it could be an internal hemorrhoid. These do not always cause itching or pain, and do not lead to any serious problems later. The trace bleeding may come and go, but should go away completely when your son has easier BM's, which is why I recommend more fiber in his diet. If there is alot of blood, the bleeding soes not go away, or your son has any symptoms that worry him or you, the he should see his doctor again.
Louise Sivak, M.D.