An oil truck tipped over, lit on fire, melted the steel in the overpasses (same level, above, and below). Bids were put out; you got a bonus if you got it done in under a month, and then for every day before that, further bonus. One bid came in both super low on "cost", and in time (like a week or something), and they'd make all their money on the bonus structure. Firm succeeded (lost like a day to a flat tire on a shipment, too), and AFAIK they were the firm selected for the Yerba Buena changeover. No quality issues either, although I don't know details.
For LA...
LA expo line was originally not going to reach the beach until... nowish? But something happened, and it got done years early. AFAIK, that schedule increase didn't come with a cost increase. Literally right now, my understanding is that the Beverly Hills line is getting accelerated, since there's no traffic to interrupt / work around.
Edit:
Has any government project been on time and overbudget, or are they always both over time and over budget?
AFAIK, examples are: 1) The east bay bridge ramp repair after that tanker fire 2) The Culver CIty <-> Santa Monica portion of the LA Expo Line
AFAIK, both of these finished early and the first one "under budget".