Is it possible that the HSA contribution was through your wife's employer, reported with code W in box 12 of her W-2, and the increase in your AGI that results from entering the code-W amount and it needing to be treated as taxable income causes you to become eligible for an increase in some kind of tax credit, an increase that is greater than the 6% penalty on the excess HSA contribution? Does the refund amount increase even more if you indicate that the excess HSA contribution will be returned?
If the contribution is instead a personal contribution, do you see any deduction for it on Schedule 1 line 13?
Compare Form 1040, Schedule 1 and Schedule 2 with and without this HSA contribution entered.
