So, I know this isn't exactly a bug, but I'd like to bring up the Officier's Pistol.
I just had a gal lose roughly 40HP though 80% pierce and 35 armor. So basically it hit for somewhere around 100 damage as a basic pistol class weapon. The backwards alien rank system just makes it a gimmick in a gal's hands, and a totally out of curve super weapon in the hands of an enemy grunt. If the guy hadn't walked most of his TUs away, and she wasn't wearing the heaviest armor I can field, she probably would have died.
I've been trying to come up with some sort of solution for it, like having an enemy version which has to be manufactured into a Piratez version so they can use different damage maths, but I don't know if it's possible to prevent the gals from just using the reversed version as their own super-grunt pistol.
Failing that, is there any way of having a "recovered as" flag for items? I'm pretty sure it exists for corpses, but I don't know how extensive it is. That would still allow gals to briefly use the backwards version in battle, but then it would correct itself upon transport back to the hideout.