By now, coach, you surely realize that not all officials will always call perfect games. And while you are correct on all five counts, it will be difficult to get the refs to get together an confer on a call without using a time-out to do so. By the time you have a quarter break or dead ball to discuss it, it will likely be too late to reverse it. Personally, when I coach, I usually deal with whatever mistakes are made by the officials and try to deal more with the mistakes made by my players. I have a little more control over that. Although, I can think of two times in about 8 years of coaching basketball that I got calls reversed. One was three seconds in the lane while the ball was in the backcourt (it was actually called on my opponent and I set the ref straight). The other was three seconds in the lane while shots were attempted. The ref had blown it dead, and my player made the shot, but they decided to award us the ball at the baseline instead of counting the basket.
Oh, and those were 8th grade games, not JV or V, thank God!
However, I wouldn't hesitate to talk to the refs at the half or after the game and tell them your understanding of the rule. Perhaps you can prevent them from making that mistake in the future. And certainly share it with your AD and/or assignor.