I was able to observe this issue but unable to re-create, even using the same save file. This is odd.
Using a current playthrough that was ready for the Forbidden Pit, I reset Hirge's skills. This is what I found on my first attempt:
When I first reset her traits and skills in New Garand, I went to Kingsbridge, the Deadwood and the Mausoleum. I gave her traits and skills per a typical build-out. I gave her Retribution 1, and saved enough skill points in reserve to up her Level 2. Hirge did NOT get mana from the undead until the Mausoleum. She didn't get mana from surface undead in Kingsbridge or Deadwood. The mana note failed to appear on screen.
After consistently getting mana from undead inside the Mausoleum, I upped her Retribution Skill to Level 2. Note, Hirge got mana from any undead killed, no matter who made the kill, or who damaged it with both Retribution 1 and Retribution 2. Hirge got mana even when she was unconscious and off-screen. She also got the mana from surface undead on Deadwood and Kingsbridge when I excited the Mausoleum.
I loaded a save right before skill reset and attempt to recreate the issue. It DID NOT recreate. Hirge got mana from any undead killed.
I loaded the save again, and reset Hirge's skill and traits, but only gave her INT 2 and Retribution 1 (Int 2 is required for the Skill). The mana point appeared on screen but not in her mana pool. This seems to be the negative mana issue. When her skills reset, she lost a lot of mana due to the drop in INT and PERs, giving her an unseen negative value. Her mana pool read "0". Once her mana pool was above zero, Retribution worked with her getting the correct mana from any undead killed.
I can consistently re-create the negative mana issue but can't seem to re-create the issue with Retribution not working. I don't have a save file of it not working because as soon as I loaded a save, it worked. I didn't think to save mid-map, which might have captured the issue in the code???
Could this be a loading error? I'm not sure how an error in map loading would impact Hirge but I can't think of anything else that would be so resistant to being re-created?