This year, my wife didn't fully fund her HSA contribution to help defray an overcontribution from the previous year. As a result, her Form 8889 has line 2 zero, but line 12 nonzero. TurboTax seems to be taking line 12 as line 13, with the net effect of my wife taking an HSA deduction. This seems extremely wrong, I'm pretty sure I can't take an HSA deduction just because I didn't contribute to my HSA.
The observed behavior is on TurboTax Desktop. My token number is 1094360