The following answer assumes that you corrected an excess contribution for 2015 in early 2016, and you just received the 1099-SA for the withdrawal of the excess in early 2017 (this would be normal).
You already paid your income tax on the excess contributions for 2015, because when you "corrected" the excess, you told TurboTax last year to add the excess that you had withdrawn back to your income for 2015 (on line 21 as "Other Income").
So the 1099-SA that has the code of "2" in box 3 tells TurboTax to ignore the amount in box 1 - because the tax was already paid on that - and to only include in your income the amount in box 2, which were the earnings that your excess contribution earned in the HSA before it was withdrawn.
The other 1099-SA - with the code of "1" in box 3 - is, as you know, your normal distribution.
Please enter both 1099-SA forms as is.
If, by chance, you meant that you corrected an excess contribution for tax-year 2016, then when you tell TurboTax that you will withdraw the excess before the due date, TurboTax will add the excess back to your income on lone 21 of the 1040. Normally, the 1099-SA for this distribution wouldn;t be sent to you until early 2018.
