You missed a step ...
The HSA contributions are already pre-deducted on your W-2. When you first add the W-2 (with code W in box 12), it ADDS tax (and a penalty) to your tax return, because it assumes you are NOT eligible to contribute to a HSA. Later on in the interview, you will tell TurboTax that you have a HDHP and did not have other health insurance. When you do that, it removes that tax and penalty that it gave you when you entered your W-2 (with code W in box 12).
You just have not yet completed the HSA area in the medical section of the program yet. Until you confirm that you are eligible to make the HSA contribution it is considered taxable.
