Mr. Monk and the T.V. Star - S2-E12
Trivia: Marcy, the obsessed fan of Brad's crime show, complains bitterly about his series changing its theme song. This was written as a little joke on Monk's real life fans, many of whom protested the show's 2nd season musical change from Jeff Beal's instrumental to Randy Newman's vocal theme. Newman's vocals opened this episode as usual, but after Marcy repeats her "don't change the theme song" mantra at the end, Beal's theme was brought back to play over the closing credits. It's been used at the end a number of times since.
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