TurboTax can only determine if you failed to complete your RMD if you have entered the amount that you were required to take, not from any of the details of the Form 1099-R that was entered. This is instead done in the questions that TurboTax asks after clicking the Continue button on the page that lists the Forms 1099-R that you have entered.
Perhaps the penalty that you are seeing is a tax underpayment penalty for having an insufficient amount of taxes withheld throughout the year and not anything specific to the entry of the Form 1099-R that reports your RMD.
If the penalty is appearing on Form 5329 1099-R and you completed all of your RMDs, try simply deleting the Form 5329 to eliminate any extraneous information that you might have entered. If the Form 5329 automatically reappears, examine the Form 5329 to see the details of the penalty that is appearing on that form.
