I’m not sure what exactly is the problem but I ‘fixed’ it by:
self.searchController.hidesNavigationBarDuringPresentation = NO;
self.definesPresentationContext = NO;
My guess is that UISearchController is doing something funky when it is trying to present as a navigation bar. So, this is a hack but it at least doesn’t block the user. The search bar doesn’t do the cool animation and cover up the navigation bar.