The box 12 "D" code reports the amount of your retirement plan deductions for work. That amount has already been deducted from the box 1 amount on your W-2, so the taxable income on your tax return should be correct. If the IRS accepted the tax return, the return should process.
The email from TurboTax may or may not be addressing the "D" code. Box 12 can have multiple codes, and it could be that another code was omitted from the W-2. The email from TurboTax should explain what you should do next.
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