Factual error: When Monk visits the prison for the first time, he is searched, passed, and has a mini-panic attack because people have touched him. Sharona steps forward to comfort him, and she puts her arms around him. This is a very serious breach of procedure and it is not possible for the guards to miss it, because Sharona has not been searched. It's a common technique for trying to pass contraband called 'a touch through' - a person with an item to be smuggled into the prison (drugs, usually), passes them on to a person who has been searched and is therefore 'clean'. Monk would be taken back to the guard's station to be searched again. He would not be allowed leniency because the guards happen to know or to like him - visitor ingress and egress is always done under CCTV and the guard would know he was being watched - quite possibly by someone who doesn't know who Monk and Sharona are.
Continuity mistake: In 3-7 "Employee of the Month", Joe Christie says he was with Monk when he got the news of Trudy's death. He said Monk had been laughing, and that he never heard him laugh again. In this episode Monk and Stottlemeyer get called to the scene of a crime, a women's clinic. In this episode there is a flashback to the exact same location years earlier and to Stottlemeyer getting the phone call about Trudy's death. He and Monk were working a case that day and Joe Christie was not present.
Factual error: 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.
Character mistake: When Randy Disher is having Chinese food in his apartment with his new girlfriend in 3-12 "Mr. Monk Gets Cabin Fever", he gets a fortune stating that he is going to get money from his uncle, and says that he doesn't have an uncle. In this episode Randy inherits a farm from his uncle who appears to have committed suicide, but was actually murdered.
Continuity mistake: They interview Jimmy Belmont in prison, who complains how Monk sent him there for killing Randy's uncle in 'Mr. Monk Visits a Farm.' However, in that episode, Monk tricked everyone (including Randy) into believing Randy had solved the murder.
Continuity mistake: The edition of the San Francisco Chronicle with the headline on Jimmy Cusack's death is dated April 1, 2006. However, at the end of the episode, which is a few days later, the newspaper with the front page photo of Stottlemeyer arresting Ron Neely, is dated March 24, 2006. In addition to the fact that the date of the arrest is a full week before the date of the murder, April 1, 2006 fell on a Saturday, when the episode says the murder was on a Monday night. (00:05:05 - 00:40:25)
Continuity mistake: When Sharon asks Sydney's old flame about the mugging 20 years ago, the glasses in front of them are full when they are being filmed from behind Sydney's ex, then are half empty being shown from behind Sharon, and in the next shot they are full again. (00:32:00)
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?