The amount with code "W" in box 12 on the W-2 is the sum of what your employer contributed to your HSA AND what you contributed to your HSA via a payroll deduction scheme.

This is confusing because of the use of the word "employer", but it actually makes sense because neither the employer's contribution nor your contribution via the payroll deduction scheme are included in wages in boxes 1, 3, and 5. That is, both are pre-tax dollars so they are treated the same and included together.

If you happen to make any contributions to your HSA using after-tax dollars (i.e., not through the payroll deduction scheme but by direct check or payment), then you would enter this as "your contribution" during the HSA interview. The same page that asks for your contribution will be pre-filled in with the amount with code W from the W-2. TurboTax is handling your contribution correctly.