After you file

I had $6,000 in employer contributions, and $1,500 in employee payroll contributions this past year.  My paystub confirms this, as well as my HSA year end statement and 5498.

So you can see in the turbotax screen below, that turbotax says all contributions via payroll should show up in the first box (even the help on the first box shows the same thing).  And the second box below says not to include contributions made through your employer.

However, you actually have to enter Taxable HSA employee contributions made via payroll deductions into that second box (even though the turbotax instructions specifically say not to).   I included the instructions for line 2, form 8889 as well, showing you have to enter any employee contributions here (and the only way to get line 2, form 8889 to populate is to type it in that box in the step-by-step).

I called TurboTax and the lady tried to tell me my W-2 must be wrong since it didn't include my employee contributions in box 12 (and it only had my employer contributions), but I referred her to the irs website which specifically says that the only employee contributions that will show up in box 12 are ones made through a cafeteria plan.   If you make a taxable employee payroll deduction (and not through a cafeteria plan), it does not show up in box 12 (nor should it, according to the IRS).

So you have to not follow turbo tax instructions, but rather still enter employee payroll contributions in the second box in order to get form 8889 to fill out accurately.  

The should fix the language of the second box to say:

Any contributions you personally made (including through payroll but that are not included in box 12).  

Or they could change the question to ask what line 2 of the form 5498-SA has and subtract anything in box 12 to figure out the employee contribution.

Currently the question is inaccurate and causing a miscalculation if answered correctly and you don't get your full deduction.  I thought they guaranteed accurate on deductions, but there does not seem to be any way to register a complaint for inaccurate deduction calculations.

Form 8889, IRS instructions for Line 2 (which that second box in the step-by-step populates)