TurboTax will properly flag an error if the IRA/SEP/SIMPLE box is marked when code D is present. Code D indicates that the distribution is not from an IRA. If editing the Form 1099-R to make sure that the form has been entered correctly does not correct the problem, I agree that deleting and reentering the Form 1099-R is appropriate. When asked, make sure to indicate that the amount in box 2a is the taxable amount.
