If my assumption is correct, you made an illegal edit, which you failed to mention. (I'm assuming you changed it's PID to make it shiny)
Read:
edit: You modified the IVs illegally (your IV edit broke overworld8). PKHeX is working as intended.
It appears you may have followed my template for changes without realizing it has etc in that section.
I changed up that line to hopefully make it more obvious :3