It's doubtful that TurboTax made a calculation error with regard to this. This portion of TurboTax has been working properly for a number of years. However, to reduce misunderstandings there *have* been a few changes to the wording on the HSA-related step-by-step entry screens for those married filing jointly.
If the contribution was made through your employer, your tax return will not show an HSA deduction because your employer will have already excluded the amount from boxes 1, 3 and 5 of your W-2, making the contribution pre-tax.
