Other mistake: Right before Aunt Bee wins the five dollar prize at Wally's station she talks about how she's never won anything, not even the church raffle, and right after she wins she excitedly waves the five dollar bill and says, "I've never won anything before in my life!" However, in season 6 episode "Aunt Bee on TV" the man from the IRS stated that Aunt Bee had won $4,850 worth of prizes on the game show, and even though she sold most of her prizes she kept two of them. So her statement makes no sense even for Aunt Bee.
Other mistake: Twice during the episode the actor who plays Floyd is replaced by his body double. The first time is when Floyd's driving to and away from Wally's station in the earlier scene, and the second is later, when Aunt Bee leaves Floyd's shop and we see Floyd stand up through the window.
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.