OMG thank you so much!! It was indeed the first box of the PC that was glitched, there was a bunch of glitched pokémon inside of it, which I don't know where they came from. PkHex erased them all by itself once I changed of active box in-game. Everything works just fine now!!
Thank you so so much!
I don't know how to mark this topic as solved or whatever so if someone can do it, it would be awesome, thanks!!