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: 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)
Suggested correction: It's tricky to make that determination. First off they were panicked and possibly facing death. Not to mention he was a large and powerful guy. Maybe they grab the gun and maybe they detain him. You can't fault characters for making rash decisions. He was only incapicated for a short time so it may have been risky to take that option.
Mr. Monk and the Genius - S7-E2
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.)
Mr. Monk Falls In Love - S7-E6
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.