Not sure if this is a bug or not, but recently, I've noticed that if my Captain or BOFFs get a Major Injury or Critical Injury, the injury is healed automatically when the mission ends and I either beam back to my ship, or my ship warps out into sector space.
Or maybe it's a new feature I didn't know about...?
I've noticed something similar with Ship Injuries as well. The Minor ones stay, but the Major and Critical ones disappear. Not that I don't like it this way, but I always thought you needed to visit ESD or DS9 to heal Major and Critical Injuries (or use an item).