Feel free to answer for NFL or NCAA (or high school), as you have expertise.
This not like you think inspired by the Seahawks fourth timeout, but rather the UCLA-Nebraska game. At the end of the first half, Nebraska had the ball on the UCLA 20. QB is getting sacked and throws the ball away (it actually ended up getting intercepted), but after review he was ruled down. Nebraska then leisurely lines up for a field goal with the clock stopped at 0:05, and kicks it through as time expires.
Now if the QB had been correctly whistled down originally, the clock would have kept running. And there’s no chance Nebraska would have been able to set up a FG in five seconds (they may have actually had a time out remaining, but let’s pretend they didn’t to keep it interesting). So the review ended up giving Nebraska an extra play and an extra 3 points.
What’s the right procedure for the clock when a review changes a play from a clock-stopping play (e.g. incomplete) to one where the clock should keep running (e.g. tackle in bounds)?
If there’s a review, then there’s a dead ball - and thus a stopped clock. However, the officials will then start the clock once the ball is set before the snap (as opposed to the clock starting once the ball is snapped). Nebraska would have to have their kicking team set up on the field and ready to snap the ball once the official starts the clock back up. Next time you notice this happening, you’ll see that the camera usually focuses on the ref, who will blow his whistle and do a “windmill” motion with his arm to indicate that the clock is starting.
That makes sense; in this situation the offensive team benefits from a free (partial) time out, but there’s no way to completely fix it, as the review needs to stop the clock.
But the officials don’t need to wait for the offense to get set do they? They can signal “incomplete”, maybe tell the coaches, run out set the ball down and start the clock, right? If the offense is ready to go, good, but if time runs out while they’re getting set, too bad, right?
It just appeared in this case that Nebraska was in no rush at all, and didn’t call a time out either.
If Nebraska didn’t call time out, and the referee didn’t start the clock on the ready signal, then that was an error.
Even when they start on the ready signal, however, I’ve never seen a team that wanted to get a play off quickly fail to do so. [Well, maybe that’s too strong a statement. I’ve seen some shitty-coached teams that never seem to have practiced a two-minute drill and can’t do anything quickly. But they’re exceptions, and the coaches usually get fired.] It’s not as if the officials can fake out the offense. It takes time to get the ball spotted correctly, check that the chains are in place and showing the correct down, and that the other six officials are in the right place. By the time they give the windmill signal any decently coached team should be ready to get off a snap.