I've faced with the problem after updating to Xcode 8. Every time after UI objects are deleted from the main storyboard I get the following warning:
Constraint referencing items turned off in current configuration. Turn off this constraint in the current configuration.
Seems really like a Xcode bug, my problem was that I was having several views that was unchecked
Starting from beginning :) after updating to xcode 8.1, I was having 2 warnings in one of my ViewController.xib, and the following steps helped me:
Try 2nd step before you try 1st :)
1) I cleaned the project and restart Xcode, warnings decreased to 1.
2) Select the warning, it showed me exactly which constraint is having an issue, and following that constraint in
Attributes Inspector I found (or remembered) this view was unchecked
Installed, I turned on Installed and thats all left over warning also disappeared, screenshot attached