Continuity mistake: When Andy and Barney catch up with the man who ran Fletch's truck off the road, the rearview mirror suddenly vanishes in the closeups that face the windshield on Bailey's car.
Visible crew/equipment: When Barney's reading the Sunday comic strip Andy comes in to close the jail in the courthouse, and when Otis walks out of his cell we can see the actor's chalk mark on the floor where he stands.
Answer: Those "boxes" are valences that used to be very common, before air conditioning. They allow for windows to be open during rain storms. They permit air circulation, without letting the rain in.