According to Wikipedia, the tiebreaker is to exclude the lowest of the 4 scores. Mustafina had a 45.933 and Raisman had a 45.366 just counting their 3 best routines on the day. That makes no sense--if it's an "all-around," the tiebreaker should still involve all 4 events. The qualifying score would be the most obvious tiebreaker, but because Mustafina's worst routine (13.633 on the balance beam) was worse than Raisman's worst routine (14.200 on the balance beam), Mustafina gets the bronze.
Also note that Raisman scored better than Mustafina on 3 of the 4 events.