I'm under the impression that pretty much every public transit agency has seen an uptick in overtime these past few years--the jobs available within public transit have seen an increase in violence towards them and likely don't offer competitive pay (and may not even be able to under various legislatively set pay scales), so the use of overtime is the only way public transit systems have been able to keep system running given their inability to hire sufficient new employees to keep up with required staffing levels.
In the cases of overtime abuse, I'll posit that if MTA were to implement systems to identify it rapidly, they'll find themselves blocked at the legislative level from doing so, or blocked at the union level from acting on any information provided by those systems -- ending that abuse would require legislative action to tackle it and real action would be painted as "not supporting [insert employee type here]" (whether or not it is or isn't is irrelevant in political messaging), and so is a politically difficult act to accomplish. On top of which systems to monitor against fraud are expensive and require hiring more people to run those systems, so you have to go to the legislature with hat in hand to beg for the money that can be allocated to build such a system.
(Full disclosure: I work for a company that makes "accountability monitoring" systems and they are employed extensively where fraud, waste, abuse and other "insider threats" have led to loss of life or intelligence and military mission compromise, and in private industry although every single private employer using such a system will strenuously deny it.)
