I believe that you are referring to the fact that on the Your Tax Breaks screen, the number of HSA contributions may not be what you think your contributions were - and it's not in most cases.
The amount on your W-2 in box 12 with a code of "W" is the sum of your employer's contributions to your HSA and your contributions by means of a payroll deduction program. Together, these are called the "employer contribution".
The amount that you contribute to your HSA outside of your employer (by direct payment to the HSA plan administrator) is called your "personal" contribution.
The amount of HSA contribution that shows on the Your Tax Breaks screen is only the personal contributions.
Frankly, this is confusing, but don't worry, all HSA contributions are being counted.
Also note that the "employer contribution" is not reported on the 1040, because this amount was already removed from your Wages on your W-2 by your employer. So no need for a deduction on the form because the amount wasn't in your income in the first place.
However, the personal contribution appears on line 25 on page 1 of the 1040.
