You needed to enter the amount of stimulus checks you received when you completed your tax return in TurboTax. Those payments, for the 1st two round of stimulus checks, were included in your refund in TurboTax before you entered how much you actually received. So, they are taken away from your refund once you indicate that you received them, as it should be.
The money you now owe is because of the 1st and 2nd round stimulus payments that were not properly reported on your tax return. It is unrelated to the 3rd, stimulus check, that was not reportable on your 2020 tax return.
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