According to the Japanese Pokémon Global Link website as reported by Serebii.net, thousands of people (5,954 to be precise) have been hit with bans from Online Play (Game Sync, Battle Competitions, Rating Battles, Global Missions).
Banned users will see error code 090-0212.[1,2]
The Pokémon Company has announced that they will continue their pursuit against people with edited save data.[1,2]
We urgently recommend not going online until we have more information on how these bans were triggered.