I don't think that it is common, but you will want to enter both sets into TurboTax. Both local districts aren't able to tax you at the same time. Here's why: NYC only taxes the NYC resident working in NYC. Since you are a Yonkers resident, you are not taxed in NYC. Yonkers does tax you if you either live in or work in Yonkers. So if you had both NYC and Yonkers tax withheld, you should get a full refund of what you paid in to NYC. But you must add both sets of numbers in boxes 18-20 on two separate lines so that this can calculate.
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