Thanks for sending me the save file, but after I tested on my own, I didn't see anything wrong when starting this battle here. Maybe it has something to do with the data decryption thing?
Edit: I did some test by using the data decryption thing and yes, now I'm pretty sure it's the data decryption which caused this glitch. The routine I used there is not compatiable with the data decryption. Also, it also means this save file will not be compatiable with the mega episode and darker future episode, because there are routines related to the party changing thing and they will mess up the decrypted Pokemon data for sure.
Thanks to jiangzhengwenjzw's help, the patch was updated for fixing two major glitches:
The movepool of some Pokemon can't be read by the system completely.
The difficulty system might mess up the moveset of several trainers.
Also, the compressed cries were replaced by better ones. The compressed ones were used to save more free space just in case more content to be added, but now it seems that I need to focus on fixing the glitches, then there should be no plan to add too much new content, so it's better to change them.
Download link of the updated Beta 5.06:
https://www.mediafire.com/file/p8yhzquxtmi6bdu/Pokemon+Nameless+Complete+Beta+5.06.zip/file