Same issue for me recently!
bot flaked and stopped botting early this morning. since i was botting localy i logged into my phone an hour after seeing the bot stopped, like a moron! only to discover i was banned! lucky it wasn't a perm ban it was just a soft one. How ever this ban was different. I could collect at stops and battle in gyms. just couldn't catch pokemon (as you normally cant in a soft ban as they run away after the first throw).
it would appear to me that niantic has changed the way they soft ban.
This "new soft ban" either lasted for 4 hours or for 18 pokemon runaways. not sure of everything that may have been affected, i was a little nervous to try a whole lot.
i just thought i give a heads up to those who may have questions or receive some input from those who may have experienced this.