I agree with you that it is not being done correctly. It seems Turbotax is not adding the amount that you took out more from one IRA and comparing it with the one you took out less wherein you took out in total what is required. On 1099-R under section RMD I checked entire gross is RMD and entered the same amounts in the RMD excess accumulation worksheet in A & B as what I entered on line 2a of the 1099-R. It is not correct, but it seems like the only way to avoid the extra tax in Part IX of Form 5329. Hopefully Turbotax will correct their calculation.
