Continuity mistake: When Natalie arrives at the marina she is wearing a long trench coat but after she discovers the dead body in the water she is wearing a short one.
Continuity mistake: When Linda is showing the apartment to the Captain, she has her phone in her left hand and crosses her arms. Her arms stay crossed, but then in a later shot, with her arms still crossed, the phone is in her right hand.
Continuity mistake: When Jay pulls up to the marina, he parks at an angle and quickly jumps out and then we see him take off in his boat. When the Captain arrives, Jay's car is no longer at an angle and is parked properly.
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