Mr. Monk Joins a Cult - S6-E11
Trivia: The cult leader, Ralph Roberts, is played by Howie Mandel of Deal Or No Deal, who suffers from OCD in real life.
Mr. Monk and the Daredevil - S6-E7
Trivia: The doctor that calls Joey is named "Dr. Levine", which seems to be a nod to Ted Levine, the actor who plays Captain Stottlemeyer.
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