Instead of a city tax return, you should file Form 10A with the Regional Income Tax Agency (RITA), which handles the tax administration for Youngstown. On this form, you can select the reason for the refund as "Withheld by Mistake" and enter your work address. You will also need to have your employer sign the "Employer's Certification" section of the form to verify that you did not actually work within the Youngstown city limits.
Further, if your employer is still withholding them, you should ask your payroll department to stop the withholding.