First, if you withdrew the entire excess contribution in a timely manner, then you will not pay a penalty. However, you will pay income tax on that amount, since TurboTax adds it back to Other Income.
Second, your HSA plan administrator will issue a 1099-SA in early 2018 for this transaction, because they need to tell you how much the earnings were on the excess contributions while they were in the HSA. The 1099-SA will have a code that will tell TurboTax to add only the earnings to your income for tax year 2017 (since you will have already paid the tax on the excess itself in 2016).
