Continuity mistake: When Mr. Monk enters the Sheriff's office, he is seen straightening out the shades on the front door, so that they are both even about half way down the window. When the Sheriff opens for the woman that was concerned about her relative, in the first shot the right window shade is now pulled all of the way down. Then, when the Sheriff closes the door, both of the shades are now even once again about half way down the window as before.
Continuity mistake: The shots don't match when Monk gets out of bed to go out and confront the UFO enthusiasts. The position of the bed covers changes noticeably between the close-up and the wider shot. (00:36:20)
Continuity mistake: When the gunman is shooting at the Jeep, he hits and deflates the near side rear tyre. His only shot after this wounds the sheriff. Yet when Monk is walking next to the Jeep, both tyres on this side are flat. Then when Monk starts going for help, the two tyres on the other side are now flat.
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