So far, I like Chuck's interpretation - 3 seconds ran off the clock
However, if you have no idea - no time should run off, and the basket should still count. Team A will have a throw-in with 4.2 seconds left on the clock.
Couple of suggestions:
(1) This is an NCAA game, so you should have a shot clock. In this scenario, the shot clock would have been turned off, leaving the shot clock operator free to have a back-up clock or to at least keep a close eye on the timer/clock.
(2) Have the timer check the clock - perhaps he pushed a button and there was a short - his display ran, but the main clock didn't. Or, maybe he started the timeout timer - both can be used as definite information.
(3) Other than for substitutes and the like, the horn (or lack thereof) should never come as a surprise. Let's face it - plenty of timers and scorers (especially the lower the level you visit) are volunteers who got roped into the job and have little to no idea what they're doing. (Mick does bring up a good point as to home clock operator - I had a nightmarish case in IM where a player's girlfriend was the clock operator.)
(4) Kill the timer after the game.
