Incorrect PP data in box for Pokemon Y save

[Dragon1065]

For some reason whenever I open up my save in the program it reads some of my Pokemon as how they were the moment I caught them but before they went to the box, and they're PP information is displayed incorrectly. It's only happened for some of them and there doesn't seem to be rhyme or reason for which ones are affected. They're completely fine in game too, so I don't know why I keep seeing this happen.

[Kaphotics]