Bug in PKHeX Or Normal?

[PLAFiles]

On Omega Ruby, I am playing a 100% legitimate playthrough and plan to eventually 100% the game. Occasionally, I put the .sav into PKHeX to check exact playtimes and stuff as I write down my journey and what I did that day.

 

I clciked on "Verify All PKMs" and I was very shocked to see it didn't popup with "Clean!" I checked and got this:

Quote

 

Invalid: PID sharing for 3DS-onward origin detected.
[main @ [01] (BOX 1)-29: 0291 - Ninjask - A4D620846728.pk6]
[main @ [01] (BOX 1)-30: 0292 - Shedinja - A8FB20846728.pk6]

Invalid: EC sharing for 3DS-onward origin detected.
[main @ [01] (BOX 1)-29: 0291 - Ninjask - A4D620846728.pk6]
[main @ [01] (BOX 1)-30: 0292 - Shedinja - A8FB20846728.pk6]

 

Is this a bug or expected? I evolved my Nincada to get both Ninjask and Shedinja at the same time, as the game intends. So shouldn't the button be showing me "Clean!" I don't want to not see "Clean!" anytime I put my .sav into PKHeX now. For the Checksums, I am also getting

"Invalid: 0C @ Region 04400
SAV: 57/58"

for some reason now. No idea why.

Edited July 12 by PLAFiles

[Kaphotics]

Making changes to box data will invalidate the checksums, as checksums are only updated when the save file is exported.

The duplicate detector is to highlight things for the user to investigate. Due to how Nincada->Ninjask&Shedinja works, you can easily confirm that there is 1 and only 1 duplicate, and that they are duplicate for both PID and EC. Which is legal.

[PLAFiles]

I don't recall editing anything at all, let alone box data. I wanted this playthrough to be 100% genuine and I know if anything was done on PKHeX, I didn't save the changes or out it back on the SD card. Really only use it to check exact current playthrough times then I exit out. Weird.

 

Would you be able to code an exception for Nincada/Ninjask/Shedinja to not show up on the Verify thing? If it's obtained fully legal/in-game at least

EDIT 3 days later: Hey, any update? @Kaphotics

Edited July 15 by PLAFiles