Mr. Monk and the Psychic - S1-E3
Plot hole: When Monk is looking for the pebble, he immediately makes an announcement through the shop's speaker system and then directly asks the guy wiping the floor where the rest of the garbage is. Given the size of the trash can it is not realistic that the guy wiping could have filled the trashcan, emptied it and have it filled half again in the 2 to 10 minutes that might have passed since the pebble got lost.
Mr. Monk Goes to the Carnival - S1-E5
Plot hole: It makes no sense why the police haven't done the most obvious thing and checked for fingerprints on the murder weapon (the knife). It would not only back up the detective's claim that he did not stab the victim (he never touched the knife) but would have given the police a major clue to finding and prosecuting the murderer.
Mr. Monk Goes to the Asylum - S1-E6
Plot hole: Monk and Manny go on the roof through Manny's window to grab a piece of cloth. Due to the possibility of suicide, it is highly unlikely that an asylum would have a window that goes directly to the roof, unlocked.
Mr. Monk and the Other Woman - S1-E8
Plot hole: Monk says that the two files, both with tab at the middle, were kept together, which led him to discover that the person related to this file is 'the guy'. In an earlier scene, when Monk is searching the file cabinets, he picks up one of these two files and tells Sharona that this file is of 'the guy'. How can he say which one of the two files with middle tabs, which are put together, is related to 'the guy'? Impossible. (00:39:00 - 00:40:00)
Mr. Monk and the Other Woman - S1-E8
Plot hole: Monk's led to the killer because he figures out that he "added a file" to the lawyer's filing cabinet, judging by the left/middle/right tabs being off. But this makes no sense on two levels - firstly why would he need to add a file? He was just replacing the real will with a forgery. He just took the old one out and added the new one, he didn't need to mess with the filing system at all. Secondly, he picks that one out because the tabs are offset, but what if the lawyer had just taken on a new client or added other paperwork? Then the tabs would be off too, but that never seems to be considered.
Mr. Monk and the Red-Headed Stranger - S1-E12
Plot hole: When Monk explains to Miss. Mass how she had murdered Sonny, a flashback of the crime shows that she isn't wearing gloves when she leaves the note to get him to go to the alley. Had the cops checked the note for prints, they would have shown Miss. Mass' fingerprints on it and knew she was responsible for Sonny's death.
Suggested correction: Just because they lifted fingerprints off the note, there wouldn't be a way to identify them as belonging to Ms. Maas if her prints aren't in the system. As a witness (and ruled out as a suspect because they thought she was blind), they wouldn't have fingerprinted her just because the found unknown prints and wanted to rule her out.
What about gun residue on the hands?
Mr. Monk and the Sleeping Suspect - S2-E7
Plot hole: Technically, Brian Babbage's plan would never have worked due to the fact that all outbound mail goes to a main post office from the local post office and then placed through scanners to determine the contents, which would have inevitably exposed the bomb inside.
Mr. Monk and the 12th Man - S2-E9
Plot hole: Monk identifies the killer because of a shirt sleeve that gets ripped off... he noticed the button is sewed on in a unique manner with the threads parallel as opposed to the "standardized" crisscross pattern. The killer and Monk coincidentally use the same dry cleaner and Mrs. Ling sews buttons parallel because it's her style. Dialogue in the episode indicated she is the only one who sews buttons on like that. But I checked over 20 button up shirts here at my house and the ratio of crisscross to parallel button sewing methods is 50% of each - hardly some unique identification method.
Mr. Monk and the T.V. Star - S2-E12
Plot hole: Unless I missed something, the killer didn't wipe his prints off the knife he used to kill his ex-wife.
Mr. Monk Goes to Jail - S2-E16
Plot hole: It is unrealistic that a prison cook who did not punch out would not be missed or found until the next day, especially after a lock-down scenario as portrayed in this episode, where a meal has been poisoned - likely in that very kitchen.
Plot hole: While convenient to the plot, the computer system used by the medical examiner is far too poor to be taken seriously for a high level agency. While Monk is unaware of deleting the files on the computer, why would there be a one button push to delete all the files on working cases? Even to not have some sort of password to delete files is questionable, as most systems in offices and workplaces will only have functions like this for administrators, executives etc. We find out that all the files are backed up and are slowly being recovered. However, these types of systems are primarily for emergency scenarios such as fire, flooding and so forth. With the ease that Monk is able to delete the files by accident, it seems a bit hard to believe how easy it is to do.
Plot hole: In this episode the police are using the toupee of the commissioner to identify the torso as the missing woman. In reality that would not be possible since cut hair is missing the root and therefore only contains mitochondrial DNA, which can only be used to identify a human's relation via the female lineage, as it is the same in relatives and passed through generations from the mother to her children. Furthermore, the identification of said torso would likely not be sufficient proof that Mr. Harley killed her as he may claim that somebody misled him to believe she was in Paris by placing the telephone call he mentioned to police.
Mr. Monk and the Employee of the Month - S3-E7
Plot hole: Monk wants to take a look at the case that got Christie to leave the force. But given that they are ordinary cops they would not be able to just go and pull internal affairs files.
Suggested correction: I'm not sure what you mean by "ordinary" cops. Captain Stottlemeyer is the one pulling the file. Plus, we don't see what they had to do to request access the files. There's no indication they just went in and randomly pulled the file with no authorization.
Mr. Monk and the Astronaut - S4-E14
Plot hole: The murderer mails a garage door opener with the button taped down to his victim and kills her by remote. But A) With the switch continuously in the "on" position, the battery would die long before the package arrived, and B) Door openers use special frequency tones that are set much like a safe combination. The likelihood of one control opening 3 different doors in the same area, as it does here, is virtually nil. (00:33:30)
Mr. Monk and the Astronaut - S4-E14
Plot hole: There is no drug in the world that could render a healthy adult unconscious for two days with a single dose, but let's go with the dramatic licence and allow that there is. Any such drug would be instantly detectable in any one of a dozen toxin screens carried out during an autopsy, and isn't someone going to wonder how a comatose woman hanged herself?
Mr. Monk and the Astronaut - S4-E14
Plot hole: The whole plot hinges on Steve Wagner knocking the victim out for 2 days, remotely hanging her while he's in space, then removing the hanging machine when he lands. But keeping someone unconscious chemically for 2 DAYS is a hell of a feat. And unpleasant though it is, she'd be voiding her bowels over those 2 days, leaving a serious mess, plus all the chemicals necessary to keep her unconscious would be found in an autopsy.
Mr. Monk Meets His Dad - S5-E9
Plot hole: Monk's dad, Jack, drives an 18 wheeler. In the scene where Jack pulls over to the side of the mountain road so they can discuss specifics about the GPS, a brake line is shown breaking and spurting what I assume is meant to be brake fluid. The rig then rolls down the mountain. However, 18 wheelers don't have brake fluid since they don't have hydraulic brakes, they have air brakes. Even if the rig lost its brakes due to loss of air pressure, the brakes are spring loaded to lock up all the wheels in this case and prevent movement. That's how you set the parking brakes, by releasing the air pressure. In other words, if he has air, he can use his application brakes; if he's lost air, he has his parking brakes set. Rigs that lose their brakes going down steep grades do so due to extreme overheating, causing brake fade, an inability of the brake shoes to grab the brake drums. This wouldn't have happened while they were parked.
Mr. Monk and the Really, Really Dead Guy - S5-E15
Plot hole: In this episode, Monk doesn't know to open a cell phone to answer it, but in "Mr. Monk and the Kid", he used a cell phone with the ransom drop with no problems. (00:04:25 - 00:05:05)
Mr. Monk and His Biggest Fan - S6-E1
Plot hole: It's out of character for Monk, a chronic stickler for details, not to correct an error, especially one relating to his own life. Marcy's diorama for "Mr. Monk & the Three Pies" includes Natalie, who wasn't around yet when "Three Pies" occurred. The doll should be of Sharona, but since that would ruin the ensuing joke, Monk is allowed to overlook it. He's aware of Marcy's unreasoning obsessions, but Monk's OCD would simply not permit him to keep quiet about a mistake that glaring.