Fragment of Dread
ATT -> Outdoor Zones -> Pandaria -> Townlong Steppes -> Achievement -> [Riches of Pandaria]

You state :
Coordinates Niuzao Temple 64.2 20.3
Inside The Ghastly Confines near Huggalon the Heart Watcher

If I create a waypoint while at Niuzao Temple using /way 64.2 20.3 then that places it in Kun-Lai.
Checking wowhead for Fragment of Dread (https://www.wowhead.com/object=213956/fragment-of-dread) the entrance to the Niuzao Catacombs is at 32.50 60.10
Checking wowhead for Huggalon the Heart Watcher (https://www.wowhead.com/npc=66900/huggalon-the-heart-watcher) the coordinates given are close at 32.9 61.7
The Fragment of Dread has 4 spawn locations. 3 in the Catacombs and 1 next to Huggalon the Heart Watcher (inside The Ghastly Confines).

It may be best if you change your description to something like :
Coordiinates Cave Entrance 32.9 61.7
4 possible spawn locations within the Catacombs/Ghastly Confines: 37.7 87.0 or 47.8 89.0 or 56.5 64.7 or 64.7 21.3

Hope this is of some use :-)

If you want to write the /way command manually, you gotta add the zone name in the command so it won't use the world map and possibly end up in another zone. It's easier to just hold down Ctrl+right click on the rare or treasure in the ATT window you want to track on the map though(right clicking on the "Rare" header will plot waypoints for all the rares listed). I got this treasure yesterday by using the coords provided by ATT, so they are indeed correct, but could add the other possible spawn locations for sure.

Same issue if I use /tway Niuzao Temple 64.2 20.3
It puts the dot in the same place as ctrl+clicking the entry in ATT. That is showing correctly for the final loot position for the Fragment of Dread - the one behind Huggalon the Heart Watcher.
The tooltip should be reflecting the extra information as to the entrance to the cave, not the same info as ctrl+clicking.
FYI. When I did this I found the item at the 3rd location after trecking through the cave system and then checking wowhead and finding out about the other 3 spawn locations.