Continuity mistake: After Frankie pays for the chewing tobacco in the drugstore, in the next closeup of Ellie the cigar box on the shelf behind her has black lines scribbled over all its identifying brand names (which is Van Dyck 43's), but when Frankie walks out the door, in Ellie's next semi-closeup that cigar box is unmarked again.
Continuity mistake: When Barney walks into the chicken coop there's a window on its door, but when Barney hides from Flint there's no such window on its door.
Continuity mistake: On Flint's farm there's a cow tied to the back fence, which can be seen in exterior shots throughout the episode - when Ellie, Andy, and Barney are there. After Flint tells Barney to get off his land, in the exterior shot when Barney walks into the barn we see that cow tied to the back fence, but next shot inside the barn we see that very same cow in the stall - note the black/white markings.
Continuity mistake: While Barney's on the farm trying to get Frankie, twice he heads into the barn through the right-side entrance door within the tall sliding double barn doors (about 12 ft high), but when it cuts to the interior shots he's entering through the barn's left-side entrance door, plus the fact that it's not within huge double sliding doors. (This interior set is seen again in "Barney Gets His Man.").
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.