Bobby: As described, BYU didn't call their timeout until it was obvious that the clock was not going to run. It should have been wound as soon as the officials got in position with the ball set, since Stanford did not have any timeouts left, or any way to stop the clock without a runoff. Even after getting the time back on the clock, it should go on RFP.
I wasn't trying to describe that; it was clear the clock hadn't run but I believe it was still going to start on the RFP. It wasn't clear why the RFP hadn't been given though. BYU definitely didn't call their timeout anywhere close to when the teams got lined up. The broadcast crew didn't do a great job of showing what was going on so it's not clear how much the officials conferenced or even when (that) the announcement was made.
Kalle: Yes, it is very likely that team A cannot do this, but if the kicker and the holder were ready to come in immediately it is in the realm of possible things...
Actually that slightly insulting rant that Upstate posted, he makes a small good point that I think is relevant here. Football clocks don't show fractions of seconds. It's therefore in the realm of possible things that had the clock started correctly, it was in fact impossible for this to happen. There could have been less time on the clock then the reaction time to the whistle (because 0:01 showing on the clock) So if we reset the clock to 0:01 we may be adding up to a nanosecond less than a full second to the clock.
Kalle: There is no direct rule support to a runoff in this situation (there is for IR)
Bobby: Although I would think replay would be able to review (but not as a challenge) since clock was all zeros.
Actually, the rule is that replay can't step in here. By rule, replay can't put 1 second back on the clock unless the next play would start on the snap which is exactly to prevent them from stepping in and doing this. I don't believe they could go to zero even if it was obvious that time should have expired but maybe I'm missing something in the rule. (Egregious error perhaps, say the USC Utah interception play from a few weeks ago had been a clock mistake instead of an inadvertent whistle?)
Upstate: Are you serious?
Yes, and in the future if you think I'm not you might want to reread my post instead of thinking that I couldn't possibly have a point and implying that in the tone of your reply. Bobby and Kalle have already pointed out what you missed.