According to a post on Reddit from a Niantic representative (and reported by Polygon), players caught using third-party services to effectively cheat the game will find themselves with a few complications.
According to the verified post by the developer:
"Starting today, Pokémon caught using third-party services that circumvent normal gameplay will appear marked with a slash in the inventory and may not behave as expected."
It's unclear exactly which apps may trigger said consequences, and what behaviour can be expected of Pokemon obtained through unofficial means.
This follows a news of an upcoming update which will change how gyms works and add raids to the augmented-reality game.