When multiple capital ships are in a fleet, the fleet leader changes every time a capital ship levels up. This means that hitting '1' to select a fleet will give you a different capship throughout the game as they level up, as will setting the fleet as a rally point. Moreover, using Tab to cycle the selected ship in the selection will not always cycle to the next cap ship in the fleet even if it is the next cap ship listed.

For example, I have a fleet that was formed around an Akkan, my first cap ship, and as frigates were added it retained its status as fleet leader. When I added a Marza, it stole fleet leadership when I purchased it levels. Setting the rally point for a new planet set the rally to the lower-leveled Marza, not the Akkan. I reselected and reformed the fleet to put the Akkan back in charge, but it lost leadership again when it leveled up in combat. Once this happened, hitting '1' selected the Marza, not the Akkan, and hitting Tab cycles past the Akkan (which was listed after the Marza in the empire tree) to the frigates.

Not game breaking, but it is incredibly annoying.