It happened to me too. I've managed to solve it by deleting the iOS DeviceSupport files.
You can try it by closing the Xcode and delete all files in $HOME/Library/Developer/Xcode/iOS DeviceSupport, then relaunch Xcode
Moshed
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This is not in code but in IB. It happens when the second view controller presentation is set to "Over Full Screen".
I managed to fix it by setting the Navigation Bar appearance