May I assume that there is a code W in box 12 of the W-2? This is the HSA contribution.
As you suspect, this code W amount should appear on the first line on the "Let's enter [name]'s HSA contributions" screen (see attached screenshot). The only thing that should appear on the second line "personal contributions" are contributions that you made directly to the HSA outside of your employer.
Is it possible that there is no code W on the W-2?
Alternatively, is it possible that you entered the code W amount on the second line of the "Let's enter [name]'s HSA contributions" and find that now it won't go away. TurboTax does sometimes hang on to numbers even after you think you have gotten rid of them.
If this is the case, then I suggest that you delete all HSA informtation and start the HSA over again. To do this, please read the following:
The safest - although brute force - way to fix this is to do the following in this order:
1. make a copy of your W-2(s) (if you don't have the paper copies)
2. delete your W-2(s) (use the garbage can icon next to the W-2(s) on the Income screen
*** Desktop***
3. go to View (at the top), choose Forms, and select the desired form. Note the Delete Form button at the bottom of the screen.
*** Online ***
3. go to Tax Tools (on the left), and navigate to Tools->Delete a form
4. delete form(s) 1099-SA (if one), 8889-T, and 8889-S (if one)
5. go back and re-add your W-2(s), preferably adding them manually
6. go back and redo the entire HSA interview.
