Yeah one of the more obvious flags completely ignored by the creators of PokeFarmer are the achievement medals, occasional speed warnings you get even when walking, level up messages, egg messages, etc - in game if you are really playing you are not able to move past that part, but with a bot you do. This should be highest priority fix to "click" them off the screen to continue in a "realistic" fashion. Until then, you are just spinning your wheels until the next ban wave - and YOU WILL BE BANNED 100%. They do them in batches, like the one yesterday, not for a particular violation at the time it happens.
