Try in Terminal: defaults delete com.apple.dt.xcode DVTSourceControlAccountDefaultsKey defaults delete com.apple.dt.xcode IDESourceControlKnownSSHHostsDefaultsKey sudo killall ssh-agent

See https://developer.apple.com/forums/thread/665666, fixed the issue for me. Specially changing to RSA SSH keys.

I am seeing it for my menus that I fill out at runtime. Seems it's doing some sort of clean up and not taking into account submenus that are empty when the NIB gets loaded.