Other mistake: When Barney is ready to pour the plaster cast into the shoe prints, there are only a few prints on the ground. There should be a continuous set of prints from the barn door to wherever.
Floyd, the Gay Deceiver - S3-E9
Other mistake: In the final scene near the end of the episode Floyd calls Andy "Andy Griffith". It's muffled, but if you listen closely it's audible.
Other mistake: Floyd's car has the license plate number "RD 757" which has been seen on other vehicles in previous episodes.
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.