There are 2 unused abilities. No Ability and Cacophony.
No Ability is presumed to be an error handler, and is used when the game manages to find a Pokémon with an ability of ID set to 00. The term isn't used in the final game because all Pokémon were given abilities.
Cacophony is an ability similar to Soundproof, which isn't assigned any Pokémon in the game. It's assumed it was meant to be the ability for Whismur, Loudred, and Exploud, given their nature for noise-based attacks.