Now a new payroll tax on every business in the New York City region has come up short by 200-million dollars.
Add it up and that means all of a sudden the agency has a 343-mllion dollar hole in its budget.
So did someone in Albany miscalculate?
"It's probably too soon for us to make that judgment. We'll be looking at that," said State Comptroller Tom di Napoli.
The state comptroller is investigating what went wrong. So far he thinks it's all because of a struggling economy, but he also says MTA estimates may have been way too rosy.
"We continue to fall short and we've been too optimistic in revenue projections in too many cases," he said.
The MTA though says this budget shortfall isn't their fault. It's Albany's.
"There's a lot of frustration, but there's not a lot be gained in yelling and screaming. Our focus is on putting that budget together," MTA spokesperson Jeremy Soffin said.
So what's the MTA to do? Could it go back to that so-called doomsday plan from earlier this year?
That plan called for eliminating the W and Z lines and 21 local bus routes.
"It would be very sad if they had to cut something because you can see things falling into disrepair already," rider Mark Dzula said.
The agency might have to cut some of its station renovation or scale back on things like countdown clocks.
Yet the agency is still promising no fare hike in 2010. At least, that is the hope.
"I hope the fares don't go up. I can't afford that," Erica Patrick said.
The MTA is now crunching its figures to present a new budget this Monday. The agency admits it doesn't look pretty.
In June, the MTA raised the price of a subway ride from $2 to $2.25. It was poised to raise fares by twice as much before the state Legislature approved a $2.26 billion bailout, but it only identified funding for the first two years of the MTA's $30 billion five-year capital plan.
Lawmakers rejected proposals to charge tolls for driving across East River bridges to help fund the agency.
The MTA operates the New York City subway, Long Island Rail Road, Metro-North Railroad and buses in the city and Long Island, a transit system that carries more than 8 million riders on a typical weekday. More than 300 million vehicles a year use its bridges and tunnels.