First, your HSA contributions are shown on your W-2 in box 12 with a code of "W", not "D".
"D" is for your contribution to your 401(k) plan.
Second, it's counter-intuitive, but both your employer's contributions to your HSA (if any) and your contributions through a payroll deduction plan are entered as one sum with the code "W",
AND this amount is called the "employer contribution".
So, when you see the screen entitled "Let's enter [your name] HSA contributions" (see screenshot below), the code W amount will be in the first line. You must not enter "your" contributions through payroll deduction on the second line because that would duplicate your contribution.
In the second line, you do enter any contributions you may have made to your HSA outside of your employer.
Now that you understand the "employer contribution" (which is part or all yours through the payroll deduction) and your contributions made outside the employer, I can tell you that in the HSA Summary, the amount with the description "Deductions" is only the amount you contributed outside your employer.
In the HSA Summary, the employer contribution (i.e., the amount with code W), is under the description of "Tax-free employer contributions".