To enter the 1099-SA into TurboTax you'll have to go to the HSA section and tell it that you had medical expenses. At that point you can enter your 1099-SA form.
The 1099-SA has a code on it in box 3. Box 3 of should be code 2 which means 'excess contributions'. If it has any other code you should contact the bank and request that they correct it.
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