You have two problems.
First, you do need to amend your 2015 return. contributions made by payroll deduction are captured from your W-2 in box 12 and should not be reported again later, you only report extra out of pocket contributions in the later interview. The amending instructions are linked below.
Second, because your 2015 tax file is wrong, you can't use it as the basis for preparing your 2016 return, or you need to make certain manual overrides. If you don't mind starting over from scratch, you would need to clear and start over, and then refuse the option to import your information from last year.
If you have a lot of things you would like to carry over besides the HSA, or you don't want to start over, then you will need to download your tax data file to your computer, purchase and install turbotax on your own computer from a CD or downloadable installer, and finish your return on your own computer. You would then override the excess contribution calculation on the HSA form. Since overrides block e-filing, you would have to print your return and mail it in.
Alternatively, if you amend first, that will require a copy of turbotax 2015 and a copy of your 2015 tax file to be installed on your local computer. After filing the amended return, if you install turbotax 2016 on your computer and open the amended 2015 file, it should transfer your data including the correct HSA information without the need for an override.
Amend https://ttlc.intuit.com/replies/3288565
