I am experiencing the same issue, which is preventing me from finishing the game. I am not able to get rid of the bugged enemy under the world in Spireton. Please help!
This is still bugged.
I explored and mapped one of the 3 islands involved in "Mapping the Archipelago: Tikawara" (the one with the Engwithan Waystation) before getting the quest and cannot complete it as a result.
Is there a resolution in sight?