If your return shows Excess HSA Contributions incorrectly, the first thing to check is that you didn't enter your HSA Contributions in the HSA interview, if they were already reported on your W-2.
The next thing to check is that you completed the HDHP section in the HSA interview. If you're using TurboTax Online, clear your Cache and Cookies, then step through the HSA interview again. This should resolve your error, since you didn't over-contribute and took regular HSA withdrawals for medical expenses.
Here's more info on Excess HSA Contribution.
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