Didn't get marks of martyrdom after a boss fight

After defeating >!Benedicta!<I noticed that I only had one mark of martyrdom despite the boss supposedly giving me three. I had moonchild equipped, which I think caused a bug to make me immortal before the fight, but I'm unsure how that would cause the marks to not drop. Is there anyway for me to fix this, or am I just screwed out of three marks of martyrdom? I've already saved past this point and Im in the next story area.