Essentially, I am having fights where every single enemy ship is dead or retreated, but I cannot force victory - The game seems to believe there is still some kind of enemy ship left on the map which is preventing me from achieving a "clean field" victory, while simultaneously the AI has not yielded the fight which would let me claim victory via the menu. The only option is to force a mass retreat on my ships and then just leave the fight - a sub optimal outcome since obviously this means you will lose salvage rewards.
This doesn't seem to be repeatable, fighting the same fight several times resulted in this happening once out of the 5 or 6 times I tried the fight, so I am not sure if my save game will be any use in this case.
Now, the only thing I can think is consistent between these occurrences is that it seems to occur when enemy ships retreat. I think it is possible some situation is occurring where AI ships which have been "manually" retreated by the AI due to being too damaged still count towards the AI's assessment of what ships it has in play - hence if it retreats a bunch of damaged or near death ships, it counts these retreated ships as being "in play" and giving it the false impression of the fight still being worth continuing.
Mods I'm using are uh, Lazylib, graphicslib, magiclib, starship legends, underworld, ship/weapon pack, nexellerin, disassemble reassamble, brdy and arsenal expansion.