did you ever solve this? I am getting the exact same warning and I too am not overriding any drawing behavior and am also getting this message on close...
Edit: I am running iOS 10 beta 5 and XCode 8 beta 5
No, seems to be a bug in iOS. But it does not seem to be critical. Though - I believe - that sometimes the area below the UIAlertController is not correctly drawn. I can see for a short period of time a black background flashing although the background of the underlying view is not black.
The only option for me to solve this is to remove the animation from the popover seque and from the self.dismiss (if you are dismissing the popover programmatically).