I've been going back though my Z-A saves, particularly those from before I did any editing, to see which pokémon were still being marked as invalid now that we're some way out from the release and most of the obvious legality edge cases are resolved.
I've found three, all relate to crossovers between sectors.
The Watchhog is a static encounter from the "The Burning Gaze of Watchog" mission. The encounter database has its location as Autumnal Avenue, but it can also be caught while standing in the adjacent Magenta Sector 2.
Similarly Diggersby is from "Underneath the Holovator" mission. Encounter database has Vernal Avenue, but Vert Sector 9 is also possible.
Finally Pansear was caught from this spawner in Jaune Sector 5:
The red line marks the transition between Sectors 5 and 8, and it's possible to catch it in the latter as I have.
All three show as legal if I change their caught location to the "correct" sector.
0505 - Watchog - E2A21CE36BF7.pa9
0513 - Pansear - DAB9D908124D.pa9
0660 - Diggersby - 8EAFDAECD07F.pa9