This isn't a bug. NPC companions accrue injuries when knocked unconscious, whether they are in your active party or not. After enough injuries are accrued, NPC companions will die permanently -- again, whether they are in your active party or not.
If you have "[c]ompletely ignored her", then Xoti is very likely at a low level and has poor equipment. Since NPCs do not level up unless added to your party, she has very likely been rendered unconscious in multiple ship battles, particularly as you have engaged higher level crews. Thus, if it happens sufficiently many times, she is gone for good.
This applies to all NPC companions, not just Xoti. It also applies to the PC, although of course it's game over in that event.
To avoid this, add her to the party, rest to clear any existing injuries, and level her up. Equipping her with better gear from your supply of spare equipment will help too.