Plot hole: If you use a Pokedoll against the Marowak Ghost in the Pokemon Tower, you can actually skip the battle and progress through the game, without ever getting the Silph Scope. This make no sense, you skip a large portion of the game this way. Just as an example, after skipping the Ghost, you fight Jesse and James with evolved Pokemon, but if you go to get the Silph Scope after this, they will be there, with unevolved Pokemon.
Other mistake: At the beginning of the game, Oak gives you a Pikachu. By this time, Pikachu is in a Pokeball. When you fight against Gary, however, the Pikachu doesn't come out of a Pokeball, like in the rest of the game. However, in this battle, he should come out of his Pokeball.
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