Defense encroachment called too late.

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Fed Rules.

In a varisity game, a newer official called defensive encroachment as a live ball foul after the play has started. Obviously, this is a dead-ball foul using NFHS rules and the play SHOULD have been shutdown. After the play, the crew discussed how to enforce the penalty. On the play, the runner gained three yards. The crew enforced this as a live ball foul from the previous spot and replayed the down.

This happens quite often with newer officials at the lower levels. How would you enforce (or not) this in a varsity game?