MikaCookies

Recently I made a backup of my saves and store them to the computer so as not to lose them and I checked them with Pkhex. However, I saw that PkHex marked two of my Pokémon as illegal, and I obtained them normally in the game. Both have in common to have been get in the trees, with Headbutt and in Mt Silver.
The game is from Pokémon HGSS and the Pokémon are Heracross and Ambipom. If I look what is wrong in the Pokémon says: "The type of encounter does not match the encounter"
What can be happening?

I'm going to attach the PKM file of both Pokémon so it is easier to know what happens

0214 - HERACROSS - 7781C2335EF1.pk4 0424 - AMBIPOM - 8A82391E1C11.pk4

I am not sure to know how to do that...

I know i can't delete NPC contacts legally, but i don't know how to do it with pkhex.

I need to delete some contacts because I use a bot that makes random encounters for me to get shiny Pokémon and every time I reive a call It froze.

Are any form to do it or is not possible yet?