The train schedule overhaul reduced the numbers of cars on a train from 12 to eight on some of the trains.
The changes contributed to crowded platforms with rush-hour riders saying the trains are packed and some connections to shuttles are not taking place.
"I think it's a little tedious sometimes," one rider told News 12. "I always like to make sure that I get on the direct train to Penn Station instead of transferring at Jamaica."
Officials were taking a look at how traffic patterns changed since the new schedules went into effect on Monday.
According to new data, 71% of peak morning riders are traveling to Penn station.
A total of 29% are riding into Grand Central Madison.
MTA officials say they will continue to monitor the traffic patterns and ridership - and make changes as needed.