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: Go to the Day-Care Man. When he asks you if you want him to care a Pokemon for you, answer YES, but in the Pokemon list, press B to cancel. He'll say "All right then, Come again." However, the "Come" shouldn't be capitalized, it should be "come". This happens because this is a shared text, so when you answer NO to his question, he'll say "Come again", and that's why it is capitalized for this text. However, it is still a mistake. This was made due to a similar text error in Red/Blue, but this mistake was created.