Mr. Monk and the Panic Room - S3-E2
Continuity mistake: When the Captain and Monk are standing in front of Randy's desk, there is no bag on the table. After a cut, a black bag suddenly appears and the Captain's hands are on it. (00:15:30)
Mr. Monk and the Panic Room - S3-E2
Continuity mistake: Just after the Captain presses the button to open the panic room door, his arms are both down. When it cuts to a shot looking at him from inside the panic room, his left arm is up against the door. (00:14:10)
Mr. Monk Takes Manhattan - S3-E1
Visible crew/equipment: After Stottlemeyer swipes the keys to Captain Cage's office, when he and Disher enter Cage's office the reflections of the moving boom pole and camera operator beside the camera are visible on the glass window. (00:20:45)
Mr. Monk and the Girl Who Cried Wolf - S3-E6
Continuity mistake: When Meredith's husband has his heart attack, his head falls into the soup bowl. However, in one shot the bowl (with his head in it) is tilted; after a cut, it is suddenly flat on the plate.
Mr. Monk Takes Manhattan - S3-E1
Continuity mistake: The angle of one of the victims' heads visibly changes from shot to shot while Monk is investigating the scene. (00:05:30 - 00:06:25)
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