That is a mistake on your W2 that can be corrected on your NY state return. Non-residents of NYC are not liable for NYC taxes. Here is a NY FAQ for reference. Note the NYC residency question/answer.
When you work your NY state return be sure to indicate you were not a NYC resident. The amount withheld by NYC will be credited on your return.
Note: be sure you entered the NYC withholding from your W2 so that it shows as an overpayment.
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