I'm having the same problem with the scuttler eyes. I've got six and can get no more. I've beaten every gong multiple times, even killed the little guys that are peaced, just in case.
I did go upstairs after killing the guy but before killing all the charmed scuttlers. I came back downstairs and wiped them out eventually, but I wonder if somehow two got away?
In any event, I can live without the benefits of finishing the quest, but I'd like to clear it off my journal. Any way to do that?