What has happened is that a number has become "stuck". That is, you entered on one pass that you would withdraw $X of excess contributions in the current year, but on the next pass, you changed something in the HSA interview such that the excess withdrawn after the end of the year (line 12.B) now exceeds the calculated excess for the year.
The most straightforward way to deal with this is to do an "HSA RESET", which is a process that deletes all HSA data from your return, so that you can start over.
***HSA RESET***
***Reset***
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....