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.
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.
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.
Answer: Stottlemeyer was already upset after the phone call. He was trying to get "Kevin" (who would have to be a judge, but no further character information is given) to issue a restraining order with no evidence of needing one, except that Adrian Monk said she needs one. Kevin said he would need to "sleep on it." So it's clear they've been trying to provide protection and unable to get the results they need, which seems to be based on no one trusting Monk the way Stottlemeyer does. He's just angry that they failed to protect Linda despite all their work. Although it does feel like a scene was cut, or altered, from the show that shows the futile attempts to protect Linda which built up to his outrage.
Bishop73