Agreed. It doesn't happen here much in JV/MS/HS games, but when I referee flag on campus it happens a lot. Live ball encroachments, live ball false starts, etc. I'll talk to the official that threw it, tell him that that is a dead ball penalty, and then cover him.
I'll change the penalty to illegal formation, tell the offensive captain that he lined up incorrectly, and give the option to the defense. It's worked so far.
Then, on the very next play they'll throw a dead ball illegal motion. I love new officials.