In the Wrath of the Druids expansion, for the quest "Trade: Sweetening the Pot", one obtains the deed from a container, spoiler
I had the skill Quick Fingers, and when approaching the container, Eivor auto-looted it. However I received generic loot (e.g. coins, a yellow feather), but not the deed. The quest was active, and the quest marker was placed at the container. After looting it, no other loot prompt appeared. Odin's Sight still showed a halo where the container is located.
Saving, quitting, reloading the game, yielded the same behavior. Loading, fast-traveling away, saving, quitting, reloading, traveling back to the container, yielded the same behavior.
FIX: Removing the Quick Fingers skill via its reset prompt, and approaching the container, presented the "hold Y to loot" interaction, rather than "tap Y to loot" , and allowed me to obtain the deed and progress the quest (this was done on a save-game generated after the container had already been auto-looted once, so no future-sight was required).
It appears that having the Quick Fingers ability, bypassed the "hold Y" loot mode (which was required to obtain the deed), but flagged the container as "looted" (removing the prompt). I'm posting this for future reference if other players have a similar issue with this or other containers.
P. S. Whoever thought of free & painless skill resetting deserves a raise.