Play 1: Team A has 11 players on the field. A 1&10 @ A20. The ready for play has been given. A10 leaves the field and A20 replaces him. Before the snap, A30 leaves the field and A10 replaces him and is inside the 9 yard marks. The ball is snapped and the run gains five yards. (The defense was not confused and had plenty of time to react to the substitution)
I am not sure passing on this situation is right; hence will play the devil's advocate again.
Does A10 go just to the sideline and chat with a coach then returns to the field of play? Or does he go into the team area? If the former, we most likely have 12 Team A players on the field longer than 3 seconds. Don't we usually flag that?
How do you know that Team B is not confused, just because they don't run around like chickens with their heads chopped off? I can imagine the DB keying on A10 would be saying "WTF is going on?" but maybe not looking or acting confused.
Lastly, where do you draw the line on not flagging substitution infractions? What if a Team A departing player stepped OB over the endline and moseyed along the limit line towards his team area? That seems relatively harmless. Do we pass on that?