As part of Niantic's near-constant war against cheaters, Pokémon GO has several steps in place to ban anyone who appears to have used third-party software or mods to manipulate the game. One such measure blocks all Android phones that have been rooted (when users grant themselves 'root' access to the operating system's top-level files), as this opens up the user's device to a degree which would enable all sorts of illegal in-game activity.
This process has been slightly controversial among Android players for some time, as rooting can also be used in much more innocent ways - it allows users to delete those pesky, usually undeletable, system apps that never get used, for example - and doesn't necessarily mean that the user has any intention of cheating within the game. Things have just been taken up a notch, however, as one user has noticed that the app appears to be taking things a little too far.
A member of the XDA Developers forum revealed that his unrooted Galaxy Note 4 (which has been rooted in the past but since been entirely reset to standard settings), received an unauthorised device error inside Pokémon GO after updating the app to the latest version. With the device being set to standard factory settings, this caused a great deal of confusion, until the user eventually decided to scrub the phone's external and internal SD cards.
"What finally got it to work shocked me beyond belief. I went through the internal & external SD card, and deleted everything related to rooting (flashable-looking zips, APKs of root-related apps, logfiles, Titanium Backup, any folder with "root", "magisk" or "xposed" in its name, etc - many of them stuff I copied over from my previous phone, never installed on this one). And magically, Pokemon Go started working!
Bottom line: Pokemon Go is abusing its storage read permissions to scan the storage for evidence of rooting."
Essentially, this means that Niantic will search through your files and folders across your device and SD cards, reading their names to find any evidence of potential rooting. Other users have since tested the theory - creating a brand new blank folder entitled “MagiskManager” (a tool used for Android rooting) - and instantly received bans. This not only means that completely innocent players could receive bans without ever having any intention of cheating, but also naturally raises some privacy concerns.
Hopefully Niantic will clear things up with an explanation in the near future.