I am getting constraint warnings for my Navigation Bar's for each of my Navigation Controllers in each of my storyboards in Xcode 8.
To get rid of the warning I set the Navigation Controller's Simulated Metrics->Top Bar setting from Inferred to None and then back again, and the warning goes away. Until the next time the storyboard is opened, then the warnings come back.
My storyboard has the iPhone SE display setting, and the navigation bar's are not Translucent.