The question is did your employer actually send any taxes to NYC? Do any of your pay stubs showing taxes paid to NYC?
Bottom line if you did pay taxes to NYC and shouldn't have you should file to get those refunded.
You should enter the W2 with the taxes withheld and then in your NY return indicate that you did not live or earn in NYC. That way you get credit/refund of those taxes on your NYS return.
Here is a link with more information.
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