[Adam]

As I read this, I'm trying to think of how it happens in real life. Three seconds isn't that long. In a situation where the team is moving slowly and stalling for a last shot, those three seconds are completely irrelevant. If he noticed it before the clock started, by all means blow it dead and embarrass the timer. If he didn't notice it until after the clock started and after the point where he realized the offense was waiting to run the play, let it go. Fixing it only causes more problems than it solves, and seems to me to break the spirit of the rules.

By secretly counting down the clock, the ref put the offense at an unfair disadvantage. This strikes me as really poor game management.