Some of the farmers are actually bandits... this means different faction hits.
a farmer that is really a farmer: Your faction standing with Karana Residents has been adjusted by -2. Your faction standing with Guards of Qeynos has been adjusted by -1. Your faction standing with Priests of Life has been adjusted by -1. Your faction standing with Knights of Thunder has been adjusted by -1.
Bandits in disguise:
Your faction standing with Karana Bandits has been adjusted by -3. Your faction standing with Karana Residents has been adjusted by 1. Your faction standing with Guards of Qeynos has been adjusted by 1. Your faction standing with Highpass Guards has been adjusted by 1. Your faction standing with Circle Of Unseen Hands has been adjusted by 1.
Recommendation:
If you don't want to mess up some of these factions, stay away from all the farmers! Or at least use /con (but that may not help you if you are an evil-type trying to raise factions due to starting out low).