Neither the IRS nor TurboTax knows what your RMD should be; it's up to you and your plan administrator to handle the RMD distribution properly (as you are doing).
So, you could answer the question 'What was your RMD?" by entering an amount less than or equal to your total distribution on your 1099-R. If you enter $0, however, and have only one 1099-R to report, TurboTax will think you didn't take your RMD and generate Form 5329 to assess a penalty.
If you have more 1099-R's, you could enter $0 for one and the distribution amount for the other. Just so TurboTax knows you took your RMD. The IRS allows you to take your RMD from one account, or across several.
It's not a bug in the program, but the wording (or instructions) could be clearer.
Here's more info on IRS Requirements for RMD's.
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