The affected customers were subway and bus riders who were charged $2.90 for their fare.
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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.
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"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.
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Migrants sleeping outside, stretching around Roosevelt Hotel's block
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