No that can never happen. You misunderstood. At the end Turbo Tax just shows you the net federal and state combined. But that is only for your info. You will still get the full refund and you need to pay a tax due.
Taxes owed for the current tax year cannot be paid from a current tax year tax refund. What you see on the TurboTax Tax Home page is your Net refund. It is not indicating your taxes owed are being paid from your tax refund.
You will receive your full state tax refund from your state, assuming the state does not change your return.
And you still have to pay the federal taxes owed before April 15, 2025 to avoid a late payment penalty.
You can't pay your federal taxes with your state refund. On the summary screen, TurboTax will show you a combined total of your federal and state return amounts, but they are processed separately. When filing your state return, you have the option to receive a check (or direct deposit) or you can apply your refund from this year to your 2025 IL return.
To verify the option you chose, look at your IL tax return. Your refund amount is on Line 32.