It actually happens if that’s the only pokemon you own that has certain hms so you won’t be stuck somewhere.

from bulbapedia:

In the core series Pokémon games, Pokémon can be released using the Pokémon Storage System. However, a Pokémon cannot be released if it is the only Pokémon in the player’s party. Once the Pokémon is released, it is removed from the player’s possession and cannot be encountered again.

In Generation III and Generation IV, if the player attempts to release a Pokémon that is the only Pokémon in their party or PC that knows a certain HM move, it will immediately return. In Generation III, these moves are Surf and Dive. In Generation IV, they are Surf, Waterfall, and Rock Climb, as well as Fly in HeartGold and SoulSilver.