The IRA custodian should have issued separate Forms 1099-R, one reporting the distributions made before reaching age 59½ and another for the distributions made after reaching age 59½. If the custodian reported all of the distributions with code 1, you can claim an exception to the penalty on the amount distributed after age 59½ by entering this amount in the "Incorrect Early Distributions" box that TurboTax provides on the page that asks, "Did you use your IRA to pay for any of these expenses?" TurboTax will include this amount on Form 5329 line 2 with code 12.
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