Locality taxes are different than income taxes, which is what you're filing for Federal and State tax returns (totally separate which is why it can't be fixed on your fed or state return). Locality taxes have their own rules and are usually a flat tax, so they aren't setup to deal with reconciliations (like you do with federal and state taxes).
While most locality taxes aren't handled in TurboTax, a few are. It sounds like yours may have been and you were told you'd get it separately (let me know?) Otherwise, you'll need to contact the locality that was a mistake and ask how you request to rectify. Let me know the locality and I can find the steps for you.
Otherwise, let me know any follow up questions.