Mr. Monk and the Very, Very Old Man - S2-E5
Visible crew/equipment: In the scene where Captain Stotlemeyer is putting one of the large snakes back in the glass container, he turns and the base of his wireless microphone is visible when his jacket gets bunched up.
Mr. Monk Goes to Jail - S2-E16
Continuity mistake: One of the times the prison guard is attempting to pat down Monk, his hands are approaching Monk's abdomen. After a cut to the next shot, his hands are suddenly around Monk's lower legs. (00:05:55)
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