defeated NPC doesn't count towards nation mission

[Captain Jack]

I have had countless of requests over the years for this reason. Apparently, it is easy to miss the NPC as 21 ports are not few.
This is the same reason why this is also explained in missions faq which tells you that as long as the npc portrait appears, the npc is out there.

In short, if you CANNOT FIND an NPC, it is either:
-The npc is really gone, because the mission was open for too long (3 months I believe)
-NPC is still out there and you missed it.

[Soliel]

Mildly related, recently while ranking up a Sea Monster spawned during the mission for Stede Bonnet. After killing the SM, I ended up finding SB at a port I had already checked. I probably just missed him, but I still think it's odd that a SM spawned out of mission.

[Leo the Conqueror]

As mentioned before, it was probably left over from a previous mission if you skipped defeating the SM. They do not automatically de-spawn when you advance ranks.