Visible crew/equipment: After Barney tells Andy he overheard Dr. Benson and Ellie "talking marriage" while spying on them, Andy heads over to the drugstore. Then, when Barney enters the jail cell, we can see a crew member's fingers (at the lower right edge of the bars, behind the wall) push the cell door closed. (00:19:45)
Continuity mistake: About 20 minutes in, Barney knocks the announcement bell off the door trying to sneak out of the pharmacy, Andy comes in one minute later and the bell rings when he opens the door. You can see the bell swinging above the door.
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.