Very common situation in government contracts and dealing with consultants in general. I am sure IBM and Accenture are in there some how. NYC government could have created a small crack-team of internal IT people who could build the system for less than a 5th of the current cost. Unfortunately most organizations view IT work as something fit for mercenaries and if you ask any King who has ever had to rely on mercenar…
What they should do is just create an open bidding system for the work and make sure that the bids are well publicized, so that not only IBM and accenture will bid. And then they will pay the bid amount only when the whole system is ready and functioning according to specs and schedule.
Thus any cost overruns are not NYC's problem.
There is a million time keeping apps out there, I am sure there will be plenty of candidates willing to modify their app to the city's requirements.