After you file

So you are missing the point that there are two types of HSA employee contributions you can make through payroll.  One of which is through a cafeteria plan, and those HSA employee contributions will show up on Box 12, code W, as you rightly stated.  But as I stated, I am specifically referring to taxable HSA employee contributions made via payroll.  These do not show up in Box 12 where the employee cafeteria and employer contributions show up. 

This is the real issue and why Turbo Tax is wrong in it's question.  They (and likewise your response, which assumed it impossible for TurboTax to be incorrect) assume the only type of HSA employee contribution is through a cafeteria plan, but it is not, and they do not show up in Box 12.  I confirmed I was understanding the information correctly from the IRS website (I'll paste the w2 instructions on HSAs below, so you can see).  I confirmed with quickbooks (another intuit product) and they said it was correct that HSA employee contributions do not show up on a W2 box 12 if they are not through a cafeteria plan.  I confirmed with a CPA, who said I will know need to file 3 amended returns because I was assuming TurboTax was calculating everything correctly and never double-checked until this year, which the CPA confirmed TurboTax is asking the question incorrectly, causing the form to not put HSA employee contributions via payroll (not through a cafeteria plan) onto line 2.

I wonder how many other people got caught by this and TurboTax did not get them their full deduction because they have the wrong question.  They really need to fix it ASAP.

Again, the second box should read: Any contributions you personally made (including through your employer, but that do not show in Box 12 of your W-2).

Or again, potentially a better option would be to have the user enter Box 2 from their 5498-SA to make sure the appropriate amount gets put into line 2 of the form 8889.

Thanks for your attention to seeing that the software gets corrected to accurately reflect the two types of employee contributions and that they do not all show up in Box 12 of the W-2.