Mr. Monk Goes to the Asylum - S1-E6
Continuity mistake: The doctor says that Mr. Monk is allergic to tomatoes. In another episode Mr. Monk makes a sandwich with tomato. There is another episode in which Mr Monk is excited about square tomatoes.
Mr. Monk Goes to the Asylum - S1-E6
Plot hole: Monk and Manny go on the roof through Manny's window to grab a piece of cloth. Due to the possibility of suicide, it is highly unlikely that an asylum would have a window that goes directly to the roof, unlocked.
Mr. Monk Goes to the Asylum - S1-E6
Factual error: The woman who accuses Monk of stealing her necklace shouldn't have the necklace inside the asylum in the first place. For both safety and insurance reasons, patients in mental facilities aren't permitted to keep any potentially harmful jewelry, including pins, broaches, earrings, belts, beads and necklaces.
Mr. Monk Goes to the Asylum - S1-E6
Visible crew/equipment: When Monk is on the roof and helping the guy not to fall, you can see that he is tied off with a rope.
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