I am unable to reproduce this symptom. TurboTax CD/download and online versions both seem to behave correctly for me.
I suggest reviewing TurboTax's 1099-R summary in forms mode or in the download of the pdf will all forms and worksheets to confirm which spouse TurboTax thinks received the 1099-R.
Regardless, this message from TurboTax can probably be ignored, either by indicating that none of the distribution was RMD or by indicating that your spouse was not required to take an RMD.
