Here's why:
* Jirachi's Debut: Jirachi was first introduced in the Pokémon Ruby and Sapphire games, which came out long after the Pokémon Indigo League anime.
* Anime vs. Games: The Pokémon anime often follows the storyline of the games, but it does make changes. While Jirachi has appeared in later Pokémon anime seasons, it was not present in the Indigo League.
If you're interested in catching Jirachi, you would need to play the Pokémon Ruby and Sapphire games (or later generations that feature Jirachi) where it is a mythical Pokémon that can be encountered through specific events.