Did you enter the W-2 and the Form 1099-R in the correct section of the TurboTax program under Wages & Income?
The income from the W-2 will be reported on the federal tax return Form 1040 Line 1a
The income from the Form 1099-R for a pension will be reported on the federal tax return Form 1040 Line 5a with the taxable amount entered on Line 5b.
