TurboTax does not know what your total RMD should be, so can't calculate whether you took the required amount or not. If you know that you did, stating that your entire distribution was RMD will not incur a penalty, since TurboTax only really knows that you are required to take one by your age.
The IRS expects that you and and plan administrator are responsible for insuring that RMD is taken, and therefore a penalty is only assessed in rare circumstances. The plan owner is ultimately responsible.
Here's more info from the IRS on Retirement Plan RMD's.
@Bgreggs
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