I think that was introduced from a few version back, you shouldn't be "upgrading" those slaves unless they cam survive the process in the first place which means spending some points in their endurance first
I could check the code see if the lab's assistant skill is involved.
Yeah checking the exploration.gd it seems totally random and intended, now killing bandits belonging to the bandit faction (not strangers or captured civilians etc...) will hit your rep sometimes, the only assured factor to gain rep killing now is killing monsters or wolves or that faction as described in the code.
Also the "Pliable" trait now seems to be the best one in order to get uber loyal slaves, just give her a maid dress til she's obedient enough to sleep in your bed (but don't have sex with her just yet) if her sex devotion/points reach 90 and you had fewer than 12 sex acts total with her she loses Pliable and becomes devoted, huge skill boost and min 80 loyalty forever.