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.
Mr. Monk and the Employee of the Month - S3-E7
Plot hole: Monk wants to take a look at the case that got Christie to leave the force. But given that they are ordinary cops they would not be able to just go and pull internal affairs files.
Suggested correction: I'm not sure what you mean by "ordinary" cops. Captain Stottlemeyer is the one pulling the file. Plus, we don't see what they had to do to request access the files. There's no indication they just went in and randomly pulled the file with no authorization.
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.
