I had the same problem, with a search bar container as the misplaced element (inside a UIViewController, inside a UITabBarController). None of the other solutions I've seen worked, but I eventually managed to work around it by re-adding the layout constraint in the viewWillAppear:
[self.view addConstraint:[NSLayoutConstraint constraintWithItem: self.searchBar.superview
attribute: NSLayoutAttributeTop
relatedBy: NSLayoutRelationEqual
toItem: self.view
attribute: NSLayoutAttributeTop
multiplier: 1
constant: 0]];