At the beginning of the show when the professor is killed in the hot tub, her dog is barking like crazy. Later in the show, the detectives state that the dog must have known the killer because the neighbors said the dog was not barking.
When Jane picks up the tray to give Patrick Sr. his breakfast, there are 2 stools at the kitchen island. When she sets the tray down and walks back over to the side of the island, the stool on the left has disappeared.
Jane told Maura that Casey was reenlisting. Officers don't reenlist; they are in the service until they retire or resign their commission.
Maura tells Jane that the drowning victim had a 0.01 blood alcohol level, as well as a high level of "cannibis." Jane reacts as if the combination of the two made it easy for the victim to be held underwater. However, a BAC of 0.01 is extremely low - the legal limit in Massachusetts is 0.08. The writers probably meant to have Maura say that the BAC was 0.10, which would be considered quite high and legally drunk.
When Jane first sees Casey at the station, he is in uniform and the insignia on it is that of a full bird Colonel. Some time later while at the diner, he tells her he is being promoted to Colonel, and Jane subsequently tells Maura it is contingent on his taking a transfer. In fact based upon the insignia he had already been promoted before he ever set foot in the station.
When Maura is looking through a microscope at a hair discovered inside the victim, she pronounces it to belong to "Canis lupus", to which Jane elaborates - "A dog", and they continue to discuss the breed. Canis lupus is gray wolf not dog. Dog's Latin designation is Canis lupus familiaris. Someone like Maura with overdeveloped attention to detail would never make this kind of mistake.
When Maura is looking through a microscope at a hair discovered inside the victim, she pronounces it to belong to "Canis lupus", to which Jane elaborates - "A dog", and they continue to discuss the breed. Canis lupus is gray wolf not dog. Dog's Latin designation is Canis lupus familiaris.