As I've said, only girl left on ship has her equipment and stat points wiped - girls participating in the combat seem to behave as intended. In case it matters, I only use girls for ground missions, which means one is always left behind.
Just tested this post-quest and the only issue I wasn't able to repeat is the third one, but I'm pretty sure it happened, since Moira on level 4 has 3 stat points assigned, even though she should have only 2, since she starts at level 2.
Two more potential issues related to ground combat:
- Omega Cube resets girl's level and HP, but stats retain their higher value - dunno, could be intended considering amount of grind/luck needed to get materials for even one of them
- Heavy Armors don't seem to be accessible currently - finished whole bot quest chain and did some few combat missions on top of that, even re-rolling rewards, and never seen one