Bots are having a lot of problems with this feature, transfering strong pokes for example.
According to The Silph Road, new Pokemon Go update makes pokemon marked as favourite untransferable, so...
all that coders should do now is to add "marking" Pokemons above % of IV set by user as favourites. This would prevent good IV's from transfering and also keep Pokemons with high CP.
Hope that this problem would be solved by our lovely coders.
Cheers