I think your son should J. treat it with humor, and say to the coach before the next game, "Hey Coach, I'm on the roster, right?" with a smile on his face and a laugh in his tone. If the coach has any sense of humor at all, he will perceive it as playful/teasing and it would be a non-offensive way to double check behind him.
With him playing on two teams, it was probably J. an oversight. I personally think he should have taken the technical early on in the game, but I wouldn't call 56-39 a "blowout" because in youth basketball, the score can change dramatically in a very short time.
As a parent, I wouldn't go to him because it could make him feel defensive and that could negatively impact his perception of your son and/or his amount of playing time, whether consciously or unconsciously on the coach's part.
Let your son be his own advocate; he's at the age that he needs to get comfortable with that and remind him that (as my Nana used to always say) you catch more flies with honey than you do with vinegar.