You must have accidentally indicated or checked a box in your NYS return that you were a resident of those cities.When you scroll through your NYS return, there is a question that states New York City Residency Information for XXX. Here you will indicate that you are a non-resident. If you have a spouse, it will ask the same question for them. Then there will be a question that asks Yonkers Residency Information for xxx. Again indicate non-resident. then there will be a series of questions if either of you have Yonkers based income. Here you will also say no.
Chances are you already recorded this information but you can edit it from the final summary page. Here is the path to edit the information.
You Just Finished Your New York Return>New York City and Yonkers Information>update. Then go through the questions as i have outlined above.
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