Pokemon GO's launch and the rollout of the game thus far haven't been the smoothest in the world, and two of the big pain points for players were server issues causing lag and preventing play, and the breaking of in-game tracking, forcing players to resort to third-party apps and services to find rare Pokemon around them. As it turns out, these two things are actually related. Niantic began a campaign not long after the game's launch to drop the banhammer on all cheaters, from GPS spoofers and botters to hackers that were using third-party apps to scrape data from the servers. While it's an easy enough assumption that anybody using a mapping app could be scraping data from the game, that was not the only issue.
Players using mapping apps did so in great numbers, and those apps sent significantly more requests per user to Pokemon GO's servers than the official game. This wound up mirroring a distributed denial of service attack, a very basic hack wherein malicious hackers inundate a server with so many requests that they end up taking it down. These attacks usually involve botnets, unwitting users whose account details are stolen in order to give the hackers the ability to send requests from their account. Thus, for the sake of safety and to help keep the servers alive for legitimate players, just about everybody using any kind of third-party app ended up banned.
While the apps in question technically violate Pokemon GO's terms of service, and many of them warned users of such before letting them sign up, Niantic is giving legitimate players who didn't know the harm they were doing, a second chance. On the official Pokemon GO blog, Niantic CEO John Hanke announced that players who wound up banned for using mapping apps, but otherwise played legitimately, would find their bans lifted. Accounts that were made automatically or engaged in other kinds of cheating, like auto-battling or GPS spoofing, would remain banned. He did, of course, warn that future violations of the terms of service would result in bans of a much less forgiving and more permanent nature.