I have two 1099 one for pension income and for RMD. If I designate one as RMD, TurboTax designates my regular pension status as RMD as well. ????

That is okay.   TurboTax needs to know you received the full RMD or more.   It is a problem only if you received less than your RMD amount.  You only get penalized for not receiving enough of your RMD, so it is fine if all of your pension distribution are labeled RMD.  

Thanks for your response. I called TurboTax and support staff connected to my laptop and noted the issue. He said he is going to escalate it. Keeping my fingers crossed.