I don't know the detail on how IL deal with it in the IL Q&A section.
BUT
Illinois does not allow you to break out the IL Bond amounts when the $$ come from Mutual funds.....only if you actually hold individual IL-based bonds.
SO, you should go back to the Federal section, and edit any 1099-DIV there that has tax-exempt interest in box 12 of the 1099-DIV. On one of the pages AFTER the main form, there is one that asks what state the Exempt-Interest-Dividends came from....you do NOT break out the IL amounts at all as IL does not allow it. Instead, you select "Multiple States" for all of the $$....or "More than one state" if you are using Desktop software (that selection is at the end of the list of states).
Once properly selected that way, the question in the IL section might go away.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*