The 3 items seem to be bogus, I have both achievements and when I go to the coordinates suggested by ATT WoW doesn't give me any notice about exploring them.

To add: If you use the feature to help us figure out problems with it, thats great.
But sometimes the answer will be an unsatisfying 'cant fix that issue atm"

Same for me, i also have this Issue but already got all Exploration Points on my main

This also occurs in older maps, such as WoD -- Nagrand example (all criteria/achievement has been met for exploration)

Exploration tracking in Retail has issues likely due to phasing or other such nonsense that hasn't been accounted for or possibly cannot be accounted for using the available Blizzard API functions and is not currently reliable for this reason. Thus it is marked as Work In Progress in the ATT settings and is not required to be enabled for the Insane mode prefix.
In the future we perhaps will find a way to fix the issues, but until then it is recommended to NOT track Exploration or do so with the caveat that some areas may be bugged.