So I started reading Pokémon Adventures (also known as Pokémon Special) recently. You know if this series is supposed to be the darkest and most mature interpretation of Pokémon ever made, then why does it assume I'm stupid? (http://img.photobucket.com/albums/v640/AnimeDude360/pokemonplothole.jpg)
The building where you find Fuji's diary has been abandoned for quite some time. It's over-run with wild pokemon and looters. So it's possible no one knew it was there.