Works as intended. There are a few 'fixes' that PKHeX performs, as users screw up a lot.
When a user sets a PKM to their boxes, if the OT of that PKM is not the OT of the save file, it is NOT under the care of the OT. Thus, the PKM is under the care of the Latest Handler, which is the OT of the save file.
If the user does not have a save file loaded, a blank ORAS save file is loaded with the OT PKHeX, other trainer info, and geolocation information.
You may disable this automatic feature via Options -> Set to SAV -> Modify PKM Info (unchecked).