Nintendo released a patch for Pokémon Legends Arceus for people who were unable to get a shiny charm, even though they met all the requirements. The update brings the game up to version 1.1.1 . Here are the patch notes:
Fixed an issue where certain conditions would prevent players from obtaining the Shiny Charm even if they met the requirements. After updating the game, players who experienced this issue can obtain the Shiny Charm by speaking with Professor Laventon inside Galaxy Hall in Jubilife Village provided they meet the requirements.