Ok, how can you fix this?
Do not **ever** use your mobile device while using the bot. You cannot play the Game on two devices. We noticed that using two or more devices at the same time can produce this "bug".
What to do now?
1) Stop Pokefarmer.
2) Start Pokemon GO on your mobile device. Hit settings. Hit logout.
3) Wait 30 minutes.
4) If possible reset your IP. (restart router)
5) Login into Pokefarmer again.