Mr. Monk Meets the Godfather - S3-E5
Continuity mistake: In the scene where Monk meets Salvatore Lucarelli (Philip Baker Hall), Lucarelli is cutting up fisheads on a cutting board. Throughout the scene the fish on the table constantly change between shots. One of the notable changes is when Lucarelli is discussing the case he has for monk there is a shot of a fish, and when the shot changes you can now see the fish's head has all of a sudden been chopped off.
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