How did you enter the employer contribution for her "HSA"?
Usually this is done on her W-2 in box 12 with a code of "W".
If you entered the contribution on the screen entitled "Did your employer tell you about any other contributions" (see screenshot below), note that you need to click on "yes" in order to get the last line to appear (so you can zero it out). Yes, enter zero, not delete the entry.
In the worst case, you may have to delete the information for both of your HSAs and re-enter yours.
Delete the 8889 form and worksheets. Do this by going to My Account (at the top), click on Tools, then on Delete a Form.
Delete any "Form 1099-SA" you see, as well as any "Form 8889-T" and "Form 8889-S".
After doing this, you will need to re-enter the HSA interview and you enter your HSA and 1099-SA information.