If you have paid the IRS taxes owed, then you don't owe them anything else.
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I have the same problem. I log in to Turbo Tax and it says "$490 due for 2019"
I didn't owe federal taxes and got a small refund, I owed $698 in state tax and I paid it through turbo tax immediately after my taxes were filed.
Should I be worried? I looked in my bank statements and sure enough state pulled the money owed from my bank account.
The program doesn't get any updates when a refund is paid out or when you pay the balance due so it will always show the return as filed. This is no different than if you has printed the return and put it in a drawer ... the printed copy will always look the same ... no tax fairy will ever change the ink on the paper.