so far i could understand it, the mentioned message is actually anticipation of what will happen next day rather than consequence, so it is giving you warnings in advance.
how to deal with causes? i believe Thunthorn offered best explanation. I would add to it that I assume there is something like memory of peasants, they remember some actions for long time and only long time of hard work can change it.
the vice-versa, accumulation of region work should remove this problem for a while.
the other factor that affect things is relative quality of region stats compared to neighboring regions, similarly to satisfaction with taxes level, which depends much on neighbor's taxes.