G
It really is as simple as on the surface, and so inelegantly stated: the game is not a human, but a machine: you are being assigned the correct desired bonuses, but the fact is capable of ambiguity or confusion, because not described in-game, in the most graceful mathematical formulaic manner or language. The two distinct, separate vs. Light-Enemies gem-buffs exist in the end, in the game's internal programming, no worries. The devs. needed to hire more psychologically astute writers, and similar issues, is the only problem here, at bottom...
With Mastercrafted "Conqueror's Gem"-loaded weapons and armor (the Utility Gem, the Conqueror's Gem, with its idiosyncratic damage against described "lightly-wounded" foes - literally, meaning, foes with health from fully healthy to roughly 75% percent!...this one is inferior arguably only to the Epic Subjugator chest-piece one, in my experience and opinion...); with Precision Utility gems and Physical Resistance Armor gems tossed in, one becomes a juggernaut of pure power: my listed damage is in the millions as a "Duelist" ranged sniper-bowman, you are capable of one-shot kills vs. hardcore bosses even on Very Hard mode even; SUMMING UP, the game is not glitched, only imperfect "editorial-stylistic translation" here...