Seems this happens mainly with the mini bosses. I’ve killed naadin multiple times and it’s still not counting towards the pathfinder. I’ve noticed this happens with other mini bosses as well.
https://x.com/shullcopjr98/status/1836251877274460524?s=46
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I tend to find that if you go to where the waypoint tells you to go to when you track it on the pathfinder, as opposed to tracking the boss on the map, it will count even if it's the 'wrong' boss. Seems like some of the bosses on the map don't align with the names on tha pathfinder. The Ogre under the bridge in the Landing is a good example of this. If I remember correctly, it is mixed up with the Wizard under the waterfall in the same area.