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.
Factual error: As Monk is removing the crumbs off the keyboard, he flicks one crumb away from the backspace key. It gets flicked up and lands near the 0 button on the numeric keypad. Yet when this happens, the screen then says "Do you want to delete files?" as if he hit the delete button.
Continuity mistake: In the opening scene, the orange-and-white scarf that Paul Harley uses to blindfold Lorissa changes positions and color patterns repeatedly between shots as he escorts her from the pool to the garage.
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.
Continuity mistake: When the commissioner is getting into the car, he opens the door pretty wide. In the next shot when his hat gets taken, he's seen opening the door again.
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