Two probabilities:
1. When you entered the 1099-SA form in the HSA interview, you did not indicate that all of the HSA distributions were for qualified medical expenses.
2. You did not finish the HSA interview. Go to Personal->Deductions & Credits->Medical and click on "1099-SA HSA MSA".
Go all the way through the interview, until you are returned to the screen entitled "Your 2016 Deductions & Credits".
The issue is that the IRS considers contributions and distributions for an HSA to be taxable until there is a completed form 8889. And TurboTax cannot complete the 8889 until the taxpayer completes the HSA interview.
Many issues with HSAs are solved by completing the interview.
