You can only get the skulls (with the exception of the blind skulls) on legendary. These are the corrsponding levels
Armory=Unnamed skull Cairo Station=Thunderstorm Outskirts=Blind and I would have been your daddy Metropolis=Catch The Arbiter=Grunt birthday party. The Oracle=Famine Delta Halo=Envy Regret=Assassins Sacred Icon=Mythic Quarintine Zone=Sputnik Gravemind=Anger Uprising=Ghost High Charity=Iron Great Journey=Black Eye
Unnamed skull=strengthed enemy and ally Artifical intelligence.