Mr. Monk Is Underwater - S7-E5
Factual error: Commander Whitaker tries to drown Monk and Natalie by trapping them in the ballast tank of the submarine. The ballast tanks on a submarine are inaccessible from the interior, and wouldn't have dramatic lighting in them either.
Mr. Monk Is Underwater - S7-E5
Factual error: Monk borrows Lt. Albright's sidearm to prove a point. All weapons on a submarine are locked in a small arms locker until needed, not carried around by officers. Further, medics are traditionally not issued firearms.
Mr. Monk Is Underwater - S7-E5
Character mistake: Commander Whitaker asks what Monk and Natalie are doing on his "ship." No submarine commander would ever refer to his vessel that way. He would refer to it as his "boat."
Mr. Monk Is Underwater - S7-E5
Factual error: The standard issue pistol for the US Navy is the 9mm Beretta 92F, not the Walther P38 as shown.
Mr. Monk Is Underwater - S7-E5
Factual error: Lt. Albright shows Monk and Natalie the "USS Seattle", a "Class 4 Submarine". US sub classes have names, not numbers, so she would be Los Angeles, Seawolf or Virginia class.
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