I contributed thousands of pre-tax dollars to my HSA, but they are being reflected in 12b of my W-2 as employer contributions. Shouldn't this reduce my taxable income?

[Opus 17]

If you contribute via payroll deduction, the contributions are recorded in box 12 of your W-2 with a code letter W.  The employer is supposed to reduce your box 1 taxable wages by that amount.  That's your tax reduction--you have less taxable income.  You can't also claim a tax deduction for workplace contributions since that is double-dipping.  

When entering a W-2, your box 12 HSA contributions will be added back to your taxable income until you certify that you were enrolled in a qualifying HDHP all year.  If you skip around, you might not see that question.  You can get to it by running the full HSA interview on the Deductions and Credits page.

If you think your employer did not reduce your box 1 taxable wages correctly, you need to speak to them and maybe get a corrected W-2.