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If you do any of the following:
>use a Pokemon that is a gym leader's ace
>use a Pokemon that the champion also uses
>use a Pokemon that your rival also uses
>use a traded Pokemon
>use items in battle
>level-up beyond the highest level Pokemon of the next boss
>do not evolve your Pokemon
>use more than one Pokemon of the same type
>use less than 6 Pokemon except at the start of the game
>have greater than a 5 level gap between your weakest and strongest Pokemon at any given time
>use HM slaves
>have more than two attacking moves of the same type in a moveset
>use herbal medicine on your Pokemon
You are not playing Pokemon correctly. You need fix this and play the game as it is intended.