Mr. Monk Is on the Run (1) - S6-E15
Plot hole: *Spoilers* Monk and Stottlemeyer cook up an ingenious plan to make Monk appear dead, but how the fugitive Monk acquires his regular clothes (in place of Mitch's uniform), the bullet-proof vest and the gun is not addressed. The police are watching Monk's apartment, Disher is watching Natalie and Julie, and Sheriff Rollins is watching Stottlemeyer, leaving us to wonder just how they managed all this right under their fellow cops' noses. (00:43:00)
Suggested correction: Stottlemeyer is a police captain. The sheriff can't watch his every move, and there are still plenty of cops who are loyal enough to Stottlemeyer for him to get one of them to deliver them to Monk or leave the items somewhere for him to retrieve.
Nice theory, but there's absolutely no hint of it in the episode. The lack of any explanation creates a bit of a plot hole because it leaves us wondering.
Mr. Monk Is on the Run (1) - S6-E15
Plot hole: The D.A. says that ballistics show that the bullet came from Monk's gun. The simplest thing to do would be to look at the gun, they'd know that it hadn't been fired and was full. With Monk's OCD we know it was cleaned, and the sheriff came in right after, so Monk couldn't have reloaded it. Yet they overlook all of this.