why is HSA deduction $0 even I paid

The amount in your W-2 with code W is your tax free contribution. This amount was not included in your Box 1 income. The program is calculating correctly. 

That is correct. There is nothing that you have to correct.

The HSA contributions shown in box 12 of your W-2 with code W are called employer contributions, even though the amount was deducted from your pay. That amount is not included in your wages in box 1 of the W-2, so it is already deducted from the income that you report. You can't deduct it again on your tax return, so you do not get any additional deduction on the tax return.

• The amount in your W-2 with code W is your tax free contribution. This amount was not included in your Box 1 income. So that is in place of a deduction that you would see elsewhere in your return. The program is calculating correctly. 

another way to put it is that your gross wages were reduced by your HSA contributions and thus box 1 only shows the net. This is the way you get the tax deduction for your contributions. 

I'm confused.  If the W amount was not included in Box 1 income, then why when I subtract Box 5 from Box 1 it only equates to the D amount for 401K?  

The deduction for the HSA is already accounted for in the wages in box 1. It’s not documented separately on the W_2 like your retirement contribution.