Mr. Monk and the Miracle - S7-E9
Continuity mistake: When Natalie enters Monk kitchen with a bag of groceries, from one angle the bag is on top of the cutting board. In the side angle she is removing items from the bag on the counter. (00:17:57)
Mr. Monk and the Captain's Marriage - S4-E12
Continuity mistake: While at the crime scene in the junkyard, Monk is trying to explain things, but is unable to concentrate because one of the stacked junked cars still has a headlight in it. Frustrated, the Captain shoots the light out so Monk can continue, but as the screen pulls back the headlight is still unbroken in the car.
Mr. Monk and the Candidate (1) - S1-E1
Continuity mistake: When Mrs. St. Claire refers Mr. Monk as "Rain man", her glass is about an inch and a half full. Next time we see her the level of liquid has dropped. (00:16:45)
Continuity mistake: In the flashbacks of Sharona's uncle's fall, he's lying perpendicular to the steps, but in the photos of the incident we saw earlier, he was lying in line with them. In fact in the last flashback showing the murder his position changes again, turning from a 90 degree angle to be more like 45.
Mr. Monk and the Class Reunion - S5-E6
Continuity mistake: During the touch football game, when Natalie first throws the ball to Monk, he catches it and a guy in a blue T-shirt and jeans is running up behind him. Angle switches as Monk twists out of the way, and it's a different guy wearing black shorts instead. A few cuts later and Monk runs past the same guy in black shorts again.
Mr. Monk Gets Married - S2-E15
Continuity mistake: In the room with the memoirs, Monk turns around and reaches towards a few slightly misaligned books to take one and read it. In the closeup, it's a neatly stacked shelf.
Mr. Monk and the Missing Granny - S2-E13
Continuity mistake: Monk identifies the kidnappers' house by the pizza box outside by the bin. In the wide shot it's upside down on its corner, with "zza" just visible behind a black bag. In the closeup it's turned around, so we can see more letters, and it's moved.
Mr. Monk and the Paperboy - S2-E10
Continuity mistake: Stottlemeyer says "does that make any sense to you?" as Monk is straightening the pots on the mantelpiece - all the lid handles are horizontal. The camera cuts away for a second, cuts back, and the lid on the far right has suddenly rotated 90°, whereupon Monk straightens it to be horizontal like the others.

Mr. Monk and the Girl Who Cried Wolf - S3-E6
Continuity mistake: When Meredith's husband has his heart attack, his head falls into the soup bowl. However, in one shot the bowl (with his head in it) is tilted; after a cut, it is suddenly flat on the plate.
Mr. Monk Makes A Friend - S5-E11
Continuity mistake: The position of Gail's body moves at the crime scene from when officers cover her head with the tarp to when the Captain uncovers her a few moments later. At first, her left hand is under her forehead and covered by her hair, but then the hand is away from her head and not covered by hair.
Mr. Monk and the Other Detective - S4-E1
Continuity mistake: When the reporter is interviewing Marty's mom at the crime scene, the reporter lifts the mic to her mouth, but in the next shot the mic is away from her mouth.
Mr. Monk and His Biggest Fan - S6-E1
Continuity mistake: When the Captain is approaching the killer, a piece of wood is protruding from the cart. After a cut, that wood suddenly disappears. The cart has also inexplicably shifted to be much closer to the killer. (00:40:00)

Mr. Monk Falls In Love - S7-E6
Continuity mistake: The woman sitting and waiting, in the red with a green scarf, is sitting without anyone to the right of her. After a cut, suddenly a man appears sitting next to her on the right. (00:06:45)
Continuity mistake: The Captain hits the murderer at the end with his left hand. In the next shot of the Captain he is shaking his right hand as though that is the hand he used to hit the murderer.

Mr. Monk Joins a Cult - S6-E11
Continuity mistake: Ralph has his hand on Monk's shoulder during the applause, but after a cut, his hands are both suddenly stretched into the air. (00:21:50)

Mr. Monk Takes Manhattan - S3-E1
Continuity mistake: The angle of one of the victims' heads visibly changes from shot to shot while Monk is investigating the scene. (00:05:30 - 00:06:25)
Continuity mistake: When Linda is showing the apartment to the Captain, she has her phone in her left hand and crosses her arms. Her arms stay crossed, but then in a later shot, with her arms still crossed, the phone is in her right hand.
Continuity mistake: When Jay pulls up to the marina, he parks at an angle and quickly jumps out and then we see him take off in his boat. When the Captain arrives, Jay's car is no longer at an angle and is parked properly.
Continuity mistake: When Monk and Al are sitting to drink wine, Al grabs his bottle with one hand to pour the wine and the other hand is hanging down to his side. In the next shot, as he's pouring the wine, he's holding the glass with the other hand. In the next shot, his hand is by his side again.
Mr. Monk Gets Stuck in Traffic - S3-E13
Continuity mistake: When Monk is talking to Daniel on the radio, in the shots from inside the truck, Krystal is standing next to the open door, to Monk's left when he turns to face her. In the shots from outside the truck, Krystal is now away from the door and to Monk's right.
Suggested correction: Randy says when that uncle dies that they were never close, so his leaving him the farm comes as a total surprise. It's still a character mistake, however, Randy is established as the sort of person who could "blank out" a relative that long-lost.
Captain Defenestrator