The Permanent Citizens Advisory Committee to the MTA surveyed nearly 400 riders recently about their experience with the transition.
It found that the majority of riders say the transition is going well, however there have been some recurring issues to be addressed.
The survey found that 42% said OMNY failed to register their payment at the fare gates, 34% got charges hours or days later, and 30% believe they were hit with "extra charges," but the vendor denies that.
Others complained of long wait times for customer service and a lack of transparency.
Of those surveyed, 26% of respondents did not experience any issues.
The MTA is disputing the results of the survey and said its own research has found that transit riders are happy with the transition to OMNY.
The MTA plans to sell its final MetroCard on Dec. 31, but riders will be able to use them for at least the next six months.
At the same time, the agency is encouraging riders to transition to its new OMNY system, which allows them to pay for trips with the tap of a phone or fare card.
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Several New Yorkers claim to be charged multiple times for OMNY rides
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