Delayed Entry

[Just Curious]

How do I explain this? New score and clock personnel at the high school. Having heard, from the officials in the JV contests, that the person on the clock would 1. Fail to buzz when sub's were waiting, 2. Buzz subs in that reported late, and 3. Buzz any time the table would have a question, we discussed this at length in my pre-game.
With about 2 minutes left in a 2 point ball game, I am lead and had just given the ball to A1 for a throw-in under A's basket, when, you guessed it, the horn goes off. Sub, B6, had reported late (The 3rd time in my game), but I tell A1 to play on only to look up and see my partner wave the sub in without a whistle. With the sub coming on the court, A1 passes the ball to A2. Half the kids on the floor are engaged in the play action and the other half are watching the substitution. I blow my whistle as A2 goes up with a shot. A2 scores. I wave off the shot as no good.
Needless to say, A's coach is upset. He wants either the 2 points or a T for 6 players on the court. I only give his team the ball out again after the substitution.
Looking back on it, I would have maybe done things a little different. What would you have done?