The official Pokémon GO website has updated to include information about banning cheaters. Various methods of cheating are specifically indicated but those that have been banned by accident can appeal their ban. In the past few weeks, players of the game have been using unauthorized methods to play the game such as GPS modifiers and emulators.

Pokémon GO - Submit a ban appeal

Your account was permanently terminated for violations of the Pokémon GO Terms of Service. This includes, but is not limited to: falsifying your location, using emulators, modified or unofficial software and/or accessing Pokémon GO clients or backends in an unauthorized manner including through the use of third party software.

Our goal is to provide a fair, fun and legitimate game experience for everyone. We will continue to work with all of you to improve the quality of the gameplay, including ongoing optimization and fine tuning of our anti-cheat system. If you believe your account has been terminated in error incorrectly, you can appeal that termination through this form. For privacy reasons, please do not post appeals on social media.

Source: https://support.pokemongo.nianticlabs.com/hc/en-us/articles/225146308