If B has 12 on the field and is unaware of it and the offense has broken their huddle or is at the line I'd flag it. Team B has already committed the substitution infraction. Why let it grow into something worse?
Let's say that A comes to the line and the QB sees a formation that he knows he can't block and decides to call a TO. The reason he called the TO could be because of the extra defensive player. Are you going to flag B at that point?
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