It seems the only explanation that would make sense is the officials decided the following occcured: (i) BYU starts to shift (which was the reason the refs threw their flags, ran into the ball, and blew their whistles), (ii) UVA responds to shifting by moving themselves and starting the play by running into moving BYU players (not relevant as refs were already running in blowing whistle to call shift as erroneous false start), (iii) BYU players move 3 yards forward in response upon receipt of contact from UVA players (also not relevant for same reason as (ii) above). The Refs conference to discuss the various shifting/responding/blocking and decide amongst themselves that (i) occurred first and was erroneously flagged before or contemporaneous with the occurence of (ii) and (iii), thereby rendering them irrelevant. That's the best I can come up with without the benefit of replay (in fact, even if the replay doesn't confirm this I think this has to be the conclusion the refs came to).