did you enter your contributions on line 2 of the 8889? if not, read no further. only money you put in directly (ie not through employer or payroll deductions goes on line 2. when HSA contributions are made through payroll deductions your wages box 1 of your w-2 are reduced by this amount so that's where you get the tax benefit/deduction. the IRS specifies that these payroll deductions and any employer match are to be reported as code W (employer contributions to HSA) in box 12 of the W-2. they flow to line 9 of the 8889. the IRS thinks you contributed $16,400 to your HSA which results in an $8,200 overfunding and a $492 penalty. if you did not contribute directly, nothing goes on line 2. send amended return 1040 schedule 2 fiorm 8889 to the IRS
to rectify this issue you need to prepare an amended return removing the line 2 amounts and an explanation that states you did not contribute directly to the HSA, therefore, line 2 on form 8889 should be zero. all contributions came through my employer as shown on line 9 on form 8889. please correct your records accordingly. however, I'm surprised because in Turbotax the 5329 penalty flows to schedule 2 line 8. so it should already have been paid with the original return.
you should contact support and have them review the 8889. we can't see it. they can so can determine what took place. no sense in filing an incorrect amended return.
