Mr. Monk and the Astronaut - S4-E14
Factual error: During their examination of the crime scene, neither Monk, Stottlemyer, Sherona, Randy or anyone else in the room wear gloves or any kind of other protective clothing. They handle artefacts that could be critical to an investigation of the woman's death, including a cheque made out to her, and they hopelessly contaminate them by doing so.
Mr. Monk and the Astronaut - S4-E14
Factual error: When Monk is running alongside the F/A-22 (now just F-22), he is so close that if Wagner had throttled up the engines a bit, Monk would have been sucked into the engine air intake. Here is a video of just such an accident on the aircraft carrier USS Theodore Roosevelt (CVN-71): https://www.youtube.com/watch?v=AF55oyAJDBk.
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