Is it possible that on the screen "Let's enter [name]'s HSA contributions", you entered the amount of your payroll deductions as a "personal" contribution? This second field shows up on line 12 of Schedule 1 (1040).
However, as Annette noted above, any amount of contributions done through your employer - whether from your employer or from you by payroll deduction - do not appear as a deduction on line 12 of Schedule 1 (1040), because the code W amount in box 12 on your W-2 is removed from Wages in boxes 1,3, and 5 before your W-2 is printed.
I suggest that you remove all your HSA data and start over, in case some piece of data has gotten "stuck".
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.
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
