May I assume that you have a code "W" in box 12 of your W-2?
This is the
sum of what your employer contributed to your W-2 and what you contributed to your HSA by means of a payroll deduction.
It's
counter-intuitive, but these amounts added together are called the "
employer contribution" by the IRS. so TurboTax has to use the same terminology.
It is also possible to make contributions to your HSA
outside of your employer (i.e., sending a check to the HSA plan administrator directly). This is considered your "personal" contribution (remember, the payroll deduction is called the "employer contribution").
There is a place in TurboTax where the HSA amount is listed (on the Your Tax Breaks screen). Here ONLY the "personal" contribution is listed, which for most people is zero.
Then it appears that TurboTax is not recognizing your contribution. If this is the case, there is nothing wrong - look at the HSA Summary. If the amount of "Tax-free employer contribution"s on the Summary shows the amount in box 12 with code of W on the W-2, then TurboTax is properly handling the HSA contributions.