Mr. Monk and the Voodoo Curse - S8-E7
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.
Mr. Monk and the End - Part I - S8-E15
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)
Answer: The two men are trying to work out a secret deal between them without involving the union, which means the workers' interests aren't being represented and defeats the whole purpose of a union. The mayor would lose labor's support and Cusack's union troubles would just be starting.
Captain Defenestrator