First of all; you should not use your mobile device while using Pokefarmer.
Second advice would be not to jump too far from your last location. And then, last but not least you can easily disable "Catch Pokemons" then start Pokefarmer looting Pokestops for about ~20 minutes until it says "Received XY" and you are not soft banned anymore.
Then you can simply activate Catch Pokemons again. This is the fastest way to get rid of this.