Mr. Monk Goes Back to School - S2-E1
Deliberate mistake: When Monk is first teaching his class, the class goes for less than 10 minutes.
Mr. Monk and the Sleeping Suspect - S2-E7
Deliberate mistake: All the mail bombs are delivered in packages tied with knotted string. The USPO hasn't allowed string-tied packages since the mid-90s (they get caught in automated equipment), but since the knots were crucial to ID-ing the suspect in this episode, that fact had to be ignored.
Mr. Monk and the Paperboy - S2-E10
Deliberate mistake: When Sharona spots Disher's personal ad in the newspaper, there is a shot of it. She then reads the description of him from the ad, which matches what's on the screen, however, the second part she reads, "Seeks petite blond with no-nonsense attitude, kids ok" is not in the ad shown. (00:22:20)
Mr. Monk Gets Married - S2-E15
Deliberate mistake: Joshua Skinner hid a fortune in gold by melting it down, mixing it with ink and writing it into 947 journals. Monk's producer concedes that in real life, 947 journals would probably hold "only about $11 worth" of gold-laced ink. But the idea was so amusing that he couldn't resist using it anyway. (00:42:00)
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