Go back to the HSA section and make sure you answered all the questions- in particular, the HDHP must be answered to qualify.
I have same problem. My wife has an HSA, she contributed $7k (family) to. We have checked off she was covered by HDCP Family plan every month, not inherited, no Medicare. It keeps telling me over funded by $6k. This worked fine last few years.
Can't delete, please disregard. For others with same problem, Page asking for contributions which per-populates amount from W-2 (box 12-W) has an additional box below for contributions made through other means, not on W-2. Kept coming back with an Additional $7k. Every time I deleted kept putting it back in. Finally put "0" in box, and it saved it.
That is a good lesson - the difference between a delete and a zero.
It won't always work - to delete an entry - because, as you saw, TurboTax didn't realize that you meant to delete the number, until you entered zero.
For others reading this, note that sometimes there is no way to get back to the screen where you had entered a number in the HSA interview that you want to change. In this case, it will be faster to simply delete all the HSA data and start over.
To delete all HSA data, please do:
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.