Niantic announced via their Official Support on Reddit that they will be adding a slash to all Pokémon caught through third-party services that circumvent normal gameplay. These Pokémon may also not behave as expected.

Update on Pokémon caught using third-party services that circumvent normal gameplay

With the announcement of Raid Battles and the new battle features, we are staying true on our commitment to ensuring that Pokémon GO continues to be a fun and fair experience for all Trainers. 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. We are humbled by the excitement for all the new features we announced yesterday. This is one small part of our continued commitment to maintaining the integrity of our community and delivering an amazing Pokémon GO experience.

Source: https://www.reddit.com/r/pokemongo/comments/6ihyoi/update_on_pok%C3%A9mon_caught_using_thirdparty/