The affected customers were subway and bus riders who were charged $2.90 for their fare.
Officials say it was due to testing error by one of their vendors, Cubic, who are in charge of building out OMNY.
MTA responded to the error and said it will reimburse riders their 15 cents per transaction.
"We're grateful to customers for bringing this to our attention quickly, and apologize for the inconvenience," the MTA said in a statement.
The fare on buses and subways will go up to $2.90 on August 20.
ALSO READ | Line of migrants sleeping outside stretches around Roosevelt Hotel's Midtown block
Migrants sleeping outside, stretching around Roosevelt Hotel's block
----------
* Get Eyewitness News Delivered
* More New York City news
* Send us a news tip
* Download the abc7NY app for breaking news alerts
* Follow us on YouTube