I've spent some time trying to figure out how to get these containers to open so I can loot the quest stuff, here are some more findings:
a) the skeleton on the upper platform in Aetera's Temple wouldn't let me loot the Diary as well. No container window pops open. I learned this poking around, but I could burn this container with fire until it lost all vitality, and then it drops the Diary.
b) putting other things into the container does nothing but loses me the item.
c) I tried plugging in my PS4 controller and switching to that alternate user interface. Same problem. It does the opening animation but no loot window. Never saw the neat 'search' that is only available in that UI, but it still won't let me open the container. *side note* What is putting items into your hand.. first time I'd seen that.
d) I hired a new party member from the boat, and sent just this one guy to the temple by himself and he had the same problem opening the container.
e) I deleted my install and re-installed from Steam. Still the same problem.
Thanks