When you went through the TurboTax HSA interview, then the total amount of contributions was reported as "excess", right? And when TurboTax asked you if you wanted to withdraw the excess, you said "yes", right? And it turns out that you did withdraw the excess.
If the HSA contributions were made through your employer (i.e., appeared on your W-2 in box 12 with a code of W), then when the W-2 was printed, the code W amount was removed from Wages in boxes 1, 3, and 5 - hence these contributions are not taxable.
However, if these contributions eventually turn out to be excess, then these contributions have to be added back to income, so that this amount can be subject to income tax after all (this appears on line 8f of Schedule 1 (1040)). This is OK because you got the income when the excess when sent to you by the HSA custodian.
If you were able to withdraw all of the excess, then you will not have any additional tax (over the regular income tax) or penalties on this amount.
So if you went through the HSA interview and told TurboTax that you would withdraw the entire amount of the excess, there is nothing more that you need to do. TurboTax will fill out the 8889 correctly so you can file and enjoy whatever refund you get.
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