I can't imagine that TurboTax is including Form 5329 as the result of entering a code D7 Form 1099-R. I suggest deleting the code D7 Form 1099-R, seeing if Form 5329 disappears, then reentering the code D7 Form 1099-R.
Otherwise, if you are using the CD/download version of TurboTax you can switch to forms mode, open the Form 5329, right-click on the entry on which TurboTax is calculating a penalty and trace back to the source of the amount on which TurboTax is calculating a penalty.
