Continuity mistake: They interview Jimmy Belmont in prison, who complains how Monk sent him there for killing Randy's uncle in 'Mr. Monk Visits a Farm.' However, in that episode, Monk tricked everyone (including Randy) into believing Randy had solved the murder.
Continuity mistake: At the end, when he is talking to Natalie about quitting since he has solved an even number of crimes, Monk is peeling an orange. The peeling that he is letting dangle from the orange changes from above the counter to touching the counter and back to above the the counter, depending on the shot.
Continuity mistake: The Captain hits the murderer at the end with his left hand. In the next shot of the Captain he is shaking his right hand as though that is the hand he used to hit the murderer.
Continuity mistake: The first victim's body and the floor around her are covered with pieces of glass, but the hole in the pane of glass is only about the size of a fist, not nearly big enough to leave that much glass on the ground.
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