I just attempted to input my W-2 data and I checked Box D for 401k contributions and TurboTax is not counting it as a deductible contribution, how can I fix this?

Contributions to a 401(k) are not deductible on a tax return.  Your gross income in box 1 has been reduced by the amount of your contributions.  Notice the wages in boxes 3 and 5 are more than the wages in box 1.

401K comes out of your pay pretax and has already been deducted from the wages in box 1.  You can't deduct it again.  Do not enter it anywhere else like under deductions.  Those are only for IRA contributions.