State tax filing

Yonkers tax.  There was no question "Did you earn wages or work in Yonkers?"   The address and zip codes on the W-2 were both in Brooklyn and no other income earned.  Turbo Tax then said it appeared you earned income in Yonkers.  No way to correct that.  Did you every live in Younkers. Checked that "no".  At the end of filling out the tax return a refund of $X was due.  Electronically filed the return.  Turbo tax, after I hit the submit button, said we need another piece of information.  Were you a resident of Yonkers.  My reply. No.  The return was electronically filed and the refund was now X - $139 with the $139 going to the city of Yonkers. 

How do I get the $139 back?