TurboTax doesn't know what your Required Minimum Distribution (RMD) should be, so it may be an answer to a follow-up question after entering your 1099-R that is causing your excess accumulation message.
If you had a distribution of 10K, for instance, you can indicate that 'all of the distribution is RMD' and the 'amount of the RMD is 10K'.
This should resolve your excess accumulation issue, although you may want to delete/re-enter your 1099-R and step through the follow-up questions again.
The IRS also doesn't care how you take your RMD; whether from one account, or across several accounts. Here's more info on IRS Requirements for RMD's.