In my opinion, that's a lot of pitches for a kid his age. I still try to keep the pitch counts of my 11Us in the 30s. It could be that he is going through a growth spurt, which will make the growth plates in his elbow more susceptible to stress.
If in fact a growth spurt is coinciding with baseball season, it might be that he'll just have to take it easy this year.
It sounds like he could be cutting the ball (throwing it slightly off center) or throwing a type of slider (twisting the forearm or wrist through the release point).
What he needs to try to do is keep his forearm at a neutral angle, if not pronated (rotated counter-clockwise) through the release point.
You might want to check out this article that I wrote that talks about dealing with medial (inner) elbow pain...
There's nothing he (or anyone) can do about this. If he's throwing the ball hard enough, the centripetal force that is generated by the rapid acceleration and then rapid deceleration of his shoulders will cause his elbow to fully extend.