Visible crew/equipment: After Aunt Bee's flight lands, when it cuts to the hotel lobby there's rug on the floor extending from the front desk to the stairs, but in the next shot as Aunt Bee and her friends walk into the lobby that rug is gone (this doesn't refer to the small rug behind them). Also note the tape mark on the floor where the bellhop stops the luggage trolley.
Visible crew/equipment: When everyone is at the airport before the flight some chalk T-marks are visible on the floor, such as the one between Andy and Helen when Andy takes the picture of Aunt Bee and her friends. (00:08:45)
Opie Steps Up in Class - S8-E5
Visible crew/equipment: When Andy walks into the living room at the Hollander's house, the white tape mark is visible on the floor between Andy's and George's feet.
Opie Steps Up in Class - S8-E5
Visible crew/equipment: When Aunt Bee picks Opie up at Billy's house, while Opie tells her all about lunch we can see the reflection of the camera and crew member, on the car's vent window.
Opie Steps Up in Class - S8-E5
Visible crew/equipment: When Aunt Bee drops Opie off at Billy Hollander's house, just as Opie opens the car door the reflections of a crew member and filming equipment are visible on the door's surface.
Opie Steps Up in Class - S8-E5
Continuity mistake: When Aunt Bee drives up to the Hollander house with Opie, in the wideshot the car's rearview mirror is affixed to the windshield, but in the closeup the mirror has vanished.
Visible crew/equipment: After Andy gets the phone call about Sam's victory, when Sam is pushed to give a speech, a few white tape marks are visible on the floor near the fireplace.
Visible crew/equipment: After Emmett talks to to the diner owner about having the bus stop moved to double his diner business, when Emmett walks down the block, the reflection of the moving camera dolly is visible in the store window.
Visible crew/equipment: When Andy, Howard, and Goober walk into Emmett's shop to tell him that Sam's running for head of City Council, the shadow of the boom mic is moving on the wall behind them, at the top of the screen.
The Wedding - S8-E26
Visible crew/equipment: The night of Howard's party, when the doorbell rings and Howard opens the door for Goober, we can see a crew member's head moving in and out of the shot at the right side of the screen.
Aunt Bee's Big Moment - S8-E23
Revealing mistake: In the close-up shot of Aunt Bee in the airplane as she starts the roll for her solo flight, as she passes out of frame you can see the inside door latch hardware, revealing that the door has been left open or removed for the shot.
Continuity mistake: At the end, when Aunt Bee serves dessert her spoon and napkin are on the table, but in the next closeup of just Andy and Opie her spoon and napkin have vanished, then when Bee's seated she removes her napkin and her own dessert and spoon should still be on the table, but in the closeups of Andy and Opie they're not.
Revealing mistake: At about 1:15 into the show, as they walk past the train station ticket window, you can see daylight between the wall of the ticket window and the rest of the building, showing it's just a prop building. It's fixed the next time they walk past it.
The Church Benefactors - S8-E20
Visible crew/equipment: At the start of the finance committee meeting, when Clara walks into the office modelling the choir robe, the shadow of the boom mic is visible on the door, in the top right corner of the screen. White tape marks are also visible on the floor, as Clara twirls in the choir robe. (00:08:15)
The Church Benefactors - S8-E20
Visible crew/equipment: During the meeting with the finance committee, a chalk T-mark is visible near Howard's feet when he and Emmett demonstrate their building and safety committee proposal.
The Church Benefactors - S8-E20
Visible crew/equipment: At the start, Andy's trying to get Opie's hair to stay down, and when Aunt Bee appears on the stairs, the moving boom mic casts a shadow at the top left corner of the screen. (00:00:30)
Visible crew/equipment: When Aunt Bee heads out for her first cooking show at the studio, Andy and Opie help load Bee's car, then just as Bee walks around the front of her car, we can see the reflection of various production equipment on the surface of the car. (00:08:00)
Visible crew/equipment: When Aunt Bee comes home enraged at the butcher, a white tape mark is visible on the floor near the kitchen door (it wasn't there in a previous shot).
Aunt Bee and the Lecturer - S8-E10
Visible crew/equipment: When Andy parks the squad car in front of the house he asks Hubert about the picnic, and the reflection of the moving boom mic is visible on the windshield. (00:12:35)
Visible crew/equipment: At the end, while the foursome sit around drinking pop, in the very last shot of Howard we can see the reflection of filming equipment in the window, before the shot fades. (00:24:30)
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.