Context for those who don't play: Assigning Akashi as the flagship lets her repair other ships that aren't medium or heavy damaged outside of the docks over time. When a player is stepping away from their computer for a while, this is a convenient way to get repairs done to more ships than fit in their docks. Because it requires swapping in Akashi as the flagship and not being in the office (where you would easily see who the flagship is), it's possible to forget you put Akashi in, and think you had your combat fleet ready to go when you left.
Context for those who don't play: Assigning Akashi as the flagship lets her repair other ships that aren't medium or heavy damaged outside of the docks over time. When a player is stepping away from their computer for a while, this is a convenient way to get repairs done to more ships than fit in their docks. Because it requires swapping in Akashi as the flagship and not being in the office (where you would easily see who the flagship is), it's possible to forget you put Akashi in, and think you had your combat fleet ready to go when you left.