I’m unable to accurately reproduce this bug and I request help in tracking it down.
After a battle, open your fleet information window.
Observe the fleet hitpoints value.
Click ‘Merge Ships’.
Observe the fleet hitpoints value is now lower.
Factors I am investigating:
Is it related to multiple battles occurring in a single turn?
Is it related to losing at least a minimum number of fighters in a battle?
Is it related to losing a precise number of fighters from a squadron?