Hello!
I have a bug that doesn't allow me to take out the first 3 pokemons of my team. It also doesn't let me switch positions to pokemons within my team. For this reason, my pidgey always remains the leader. The rest of the pokemon can be removed from my team.
I had stopped playing since the process of switching between RED/BLUE to Silver.
I just started playing again yesterday and had a similar problem. I had a snorlax in my team that I had obtained in Kanto. But I was playing the Johto story.
The same error happened only with this snorlax at the beginning, but after releasing it the error moved to the next 3 pokemons that I had in the team.