Not a contradiction. I don't believe in omniscient or all powerful devices that function like literal deus ex machinas and heal everybody all the time. It was stated *plainly and clearly* that the device was used in healing terminally ill patients. They cannot undo physical damage from gunshots (the regen packs and other devices were used to heal Garibaldi's wound, and the alien device was used to raise his life energy level enough to bring him out of the coma). The emperor suffered a massive attack that destroyed parts of his heart. Can't be fixed by this device.