Probably due to the USS Freedom (aircraft carrier) and USS Liberty (destroyer) being multi-object compositions rather than single objects, if placed in Scenario phase, they will not disappear when switching to Intro or Outro phases, instead will stay with no object marker, impossible to be removed in normal, convenient means. If you go back to the Scenario phase and remove the Freedom/Liberty ships, they will still be visible in other phases and will re-appear as an non-editable object when going back to Scenario phase once again.

Eden Editor restart is required or user has to preview the scenario and go back to the editor to have the "ghosts" disappear.