Code D indicates that the contributions through your employer are elective deferrals to a 401(k) plan (or the federal TSP plan). It is not a SEP-IRA or any other kind of IRA.
Enter the code D amount only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax. Go back and remove the entry that you made under Deductions & Credits -> Retirement and Investments -> Traditional and Roth IRA Contributions.
