Turns out it wasn't the HSA at all. When filling out something from my wife's W2 she had entered a wrong letter (well, actually it was supposed to be something like..... it was bb and she entered b).
We never looked at the W2 info because we thought surely there's nothing wrong there, everything else was mostly the same minus the HSA use, which made no sense and made me think TurboTax was somehow miscalculating something.
