My 1099-R has a taxable amount listed in box 2a, which I entered into Turbo Tax. However, Turbo tax is using the simplified method to calculate its own taxable amount, which is different than the amount in box 2a. Who is right, and how do I justify it?
Unless you have reason to believe that the amount shown in box 2a of the Form 1099-R is incorrect, you should not be using the Simplified Method. If you report a taxable amount that is less than the amount in box 2a of the Form 1099-R, the IRS will bill you for taxes on unreported income and to avoid having to pay the bill you'll have to explain to the IRS's satisfaction why the amount in box 2a of the Form 1099-R was incorrect.
The calculation of the taxable amount using the Simplified Method requires accurately entering the amounts requested, and users often get the entries wrong. If you have no reason to believe that the amount in box 2a of the Form 1099-R is wrong, I suggest that you delete the 1099-R from TurboTax, reenter it, and in the follow-up indicate that the amount in box 2a is the taxable amount.