courtsey runner rule high school

Question
I coach my son's off-season high school baseball team.  During a game, a heavy set kid from the other team was walked by my pitcher, upon touching first base, his coach asked for a courtesy runner. As I understand the rules that we have been playing under (HS rules), a courtesy runner is only used when there are 2 outs and for the pitcher and catcher only.  This coach put in a courtesy runner for his heavy 1st baseman, I realized this as soon as it happened, but chose not to say anything.  The kid scored on a double by the next batter.  I called time, approached the ump, and said that was an illegal baserunner, he said, "Yeah the firstbaseman right?", he conferenced with the home plate ump, and ruled, safe, the run counted.  At the end of the game he confided in me that he did not know the ruling.
Should the run have counted?  And when would be the most advantageous time to appeal the runner?

Answer
Paul,

I don't know the rule for high school.  I wasn't able to find a standard high school rulebook on line.

However, in most instances, the correct time to appeal when there is a questionable play is before the next play takes place.  I would have filed an official protest with the umpire as soon as the pinch runner was put into the game.  That way, if ruled in your favor by the league, that's where the game would restart.  Typically once a play is over, it is in the books and there isn't anything you can do about it.

Hope this helps!

Brian