Went onto a gunboat and killed the two NPC's ontop. None spawned afterwards and was stuck at 2/3 enemies killed. Summoned my the dinghy/mini boat and re got on my main boat and it stopped the boarding action but if I restarted the boarding action it was still the same issue.
Sank the boat with my crew... before they respawned on my boat! The boat loot spawned after it sank too.