I am not certain exactly how to reproduce the issue, as sometimes it seems to happen while "just playing along" while other times it appears to happen as a result of restarting the server. I run a dedicated server off my computer for a single other friend and myself to play on. I have a "fleet" which is a single carrier ship and 96 small drone ships. My carrier ship also has turrets on it. In the initial release with Fleets, I did not notice this behavior.
Behavior: Fleet list is rearranging itself. My flagship consistently is removed from the fleet so far. A random number of the drone ships are removed, and sometimes some of the turrets are added into the fleet. Initially I created the fleet using the search functionality - thinking there might have been a bug, I've recreated the fleet each time since by scrolling through the three pages of turrets to add the ships without searching. Each turret is two ships, and sometimes both ships are added, sometimes only one is added. If the ship with the AI module is added, the AI module is deactivated, leaving me with randomly disabled turrets across my ship. Restarting the server seems to pretty consistently affect the fleet member list.
I hope this is enough information for you to see this issue as well!