Since you removed the excess contribution prior to the filing deadline you won't be subject to the 6% excise tax. If all your contributions were made via payroll deduction and you have a 1099-SA to report HSA distributions, or if you made contributions other than via payroll, then during the HSA interview TurboTax will tell you "You have excess contributions, will you remove them before the deadline?" Answer Yes. If you don't have a 1099-SA to enter, you will need to navigate to the HSA section so you can indicate your removed the excess.
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