Plot hole: Death row prisoners cannot donate organs. No doctor participates in an execution and after the lethal injection the medical examiner must wait at least fifteen minutes to test for cardiac activity before pronouncing the prisoner dead. This is enough time for hypoxia to render the heart, lungs and kidneys useless for transplant. Apart from this, organs intended for transplant must be removed within minutes of the death of the donor. Prisoners are not executed in operating theatres.
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.
Plot hole: The pharmacist's plan is really stupid. He changes all their meds so they don't work, after drinking from the fountain he changed them back so it appears the fountain healed them. The problem is if they think the fountain healed them they're not going to take their meds, so their pain would come back.
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: This episode's entire story line takes place in the six days before Christmas (Dec. 19-24). "Bad Santa" is shot in the right shoulder on the 19th, sustaining a wound serious enough to require wearing a sling for the next several days. Yet at the end, a mere few days later, he's recovered enough to have a knock-down-drag-out fistfight with Monk, wielding a knife and throwing powerhouse punches with his wounded arm as though no injury had ever occurred. (00:38:00)
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.
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.
Plot hole: *Spoilers* Monk and Stottlemeyer cook up an ingenious plan to make Monk appear dead, but how the fugitive Monk acquires his regular clothes (in place of Mitch's uniform), the bullet-proof vest and the gun is not addressed. The police are watching Monk's apartment, Disher is watching Natalie and Julie, and Sheriff Rollins is watching Stottlemeyer, leaving us to wonder just how they managed all this right under their fellow cops' noses. (00:43:00)
Plot hole: The murderer planted the voodoo dolls after the accidents to make them look like victims and cover up her murder of her uncle, but none of that was necessary! She uses an untraceable poison on her elderly uncle to make it look like a heart attack. So if he'd died...they just would have figured it was a heart attack! No suspicion would have fallen on her anyway, the entire voodoo thing was just needlessly complicated and only exists for the episode's plot.
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)
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.
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.
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.
Plot hole: It is not realistic that Miss Zladovic is confronted with the murder weapon for the first time in her flat after she had been arrested and interrogated about the same exact murder days before. It is also impossible that the police did not show her a picture of the murder victim as it is police standard to ask any suspects for connections/relations to "their" victim.
Plot hole: Monk and Natalie temporarily incapacitate Jake before crawling all the way down the hall from the bathroom to the living room while pulling a heavy claw-footed bathtub. Exactly why didn't Monk or Natalie think to consider a more permanent solution to preventing Jake from attempting to kill them again, like grabbing his gun and using it to detain him until the police could arrive to arrest him? (00:30:00 - 00:39:05)
Plot hole: When Randy tells Captain Stottlemeyer that the killer shot the train station announcer and took his jacket and ID, the microphone in the room is still active and everyone in the station hears Randy's conversation. If that's the case, then why didn't everyone in the station hear the gunshot? Even if the killer used a silencer, he would have made noise taking the announcer's jacket and changing his disguise, which would sound like a struggle over the open mic anyway, and it would make no sense to turn it on after killing the man. (00:29:00 - 00:30:00)
Plot hole: Kloster's plan of switching the headstones wouldn't have worked because cemeteries keep records of who's buried in which plot. Before exhuming the body, the records would have been checked and someone would have noticed that the name on the headstone and the name in the records didn't match. (He might have broken into the office and changed the records, but it's never brought up, so he likely didn't.)
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)