Never mind again, the problem occurred. I didn't report it right after the fact so the memory was a bit off. It's when I edit the pokemon's held item with the program. With the "Only edit" checked or not, the problem still happens, which is the first listed relearnable move occupies all 4 slots. Growlithe for example, used the program to give it a choice band, its relearnable moves all become Heat Wave.
Same thing even with editing the moveset of a pokemon, the first relearnable move takes up all slots of relearnable moves.
Should be fixed in this new version: https://github.com/drgoku282/PKMN-NTR/releases/tag/1.19.3