Form 8889 line 2 is a zero, but I had $2k withheld. Form 8889 Line 9 puts the amount I paid in on this line, not the amount my employer paid for me.

[ahkba1]

I paid in about $2500 to an HSA through payroll deduction.

My employer added $479 when I enrolled.

On the W-2 they show the combined amount on W2 Box 12c W

When it flows to TurboTax on Form 8889 is has a zero on line 2 and the full combined amount on Line 9.

No deduction is applied to the 1040 Line 25

[ghost]

This is correct. Deduction was given to you by reducing your taxable income on your W2. Line 2 does not apply unless you contribute using money that was or will be taxed.