Plot hole: The D.A. says that ballistics show that the bullet came from Monk's gun. The simplest thing to do would be to look at the gun, they'd know that it hadn't been fired and was full. With Monk's OCD we know it was cleaned, and the sheriff came in right after, so Monk couldn't have reloaded it. Yet they overlook all of this.
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.
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.
Plot hole: Monk supposedly hears for the first time that Max was not carrying anything away from the crime scene when he speaks to the witness in front of the church. This leads him to conclude that there must have been a 2nd man with Max 14 years ago. But this does not make sense given that the witness with her photographic memory did not change her testimony and given Monks ability to observe and memorize details it is very unlikely that he did not come to that conclusion 14 years ago already. (00:32:45)
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.
Plot hole: How come Monk and Natalie didn't think it suspicious that Cassie Drake was killed in her house within less than twelve hours after they had found out she was responsible for killing her patient? Since Jake and Ramone were the only two people they had disclosed their findings to (apart from Stottlemeyer and Disher), they should have focused in on Jake much sooner. (00:24:00 - 00:27:00)
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.
Plot hole: When Stottlemeyer is confronted by the Sheriff for not going to the morgue there are 2 plot holes in that one scene: first it is impossible for that article to be in the morning paper since the coast guard "just fished him out" last night. And secondly an article, especially a long article like the one about the body in the bay would contain a physical description of said body. That is the reason it does not make sense to even ask the captain why he did not go to check the body to see if it was Monk when the body was tattooed and had red hair. (00:13:30)
Plot hole: There is no other reason for Randy to hand Natalie the walkie-talkie but to fill that plot hole. He is in fact in breach of police rules when he hands his department issued radio to a civilian to answer it while he is on duty. The same goes for Stottlemeyer and the car keys he hands to Monk. Even more so since he knows Monk could not even drive that car to the side in the far fetched scenario that a police car had to be moved while the cop is serving a warrant inside the building the car is parked in front of. (00:01:15)
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.
Plot hole: When Stottlemeyer and the other cops arrive at the recycling center, the patrol car's siren turns on and off. The killer had said to Monk that if he called the cops, he'd kill Natalie. Coming to a hostage situation with the siren going would be a really bad idea. (00:37:45)