My pokemon I captured in the game are illegal

[Guts1802]

Hello, I recently started playing LeafGreen again, and when I put my save in pkhex, I saw a lot of my Pokemon get flagged with the message "Invalid: Ability does not match ability number." I'm playing a ROM that bypasses trade evolution on my 3DS. They are all Pokemon I captured in the game itself, so I don't understand why they are flagged as illegal. I tried switching the abilities of the Hitmonlee, for example, from his Limber (2) to Limber (1) and now I get "Invalid: PID+ correlation does not match what was expected for the Encounter's type." Even after putting it back to Limber (2), I still get that message. 

If anyone could help me, I would appreciate it. I've attached my save file as well.

0004000003F4E900.gbavc.sav

[Kaphotics]

PKHeX is built to support unmodified game save files. PKHeX cannot know what changes you've made to the ROM.

Since you are playing a ROM hack, the modifications by the patcher likely changed more than just bypassing trade evolutions. It probably mirrored ability slots (wrong, a single-ability species needs XX-00 not XX-XX).

Changing the ability selection will cause the program to recalculate a PID, hence the second image.

Copy the PID, then fix the ability index, then paste the original PID back.

[Guts1802]

15 minutes ago, Kaphotics said:

PKHeX is built to support unmodified game save files. PKHeX cannot know what changes you've made to the ROM.

Since you are playing a ROM hack, the modifications by the patcher likely changed more than just bypassing trade evolutions. It probably mirrored ability slots (wrong, a single-ability species needs XX-00 not XX-XX).

Changing the ability selection will cause the program to recalculate a PID, hence the second image.

Copy the PID, then fix the ability index, then paste the original PID back.

It worked, thanks.