Mr. Monk Goes Back to School - S2-E1
Other mistake: Derek tells Beth to meet in their "usual spot" the next day at 8am. The next scene has Derek sitting at his desk and it looks like the kids are already in deep with their SAT tests. Beth falls at 8:25am (as per the clock in the testing room.) There is no way that Derek could have killed Beth, put her on the minute hand (later in episode on the Monk recap, it has 8:15am. If Derek was proctoring a SAT test, I don't know of any that start around 8:20 and immediately in depth.
Mr. Monk and the 12th Man - S2-E9
Other mistake: In the scene where Mr.Babcock is murdering the woman in the cinema, we see the woman has a big bucket of popcorn. As he starts strangling her, only a small amount of popcorn falls out. When the camera turns toward the floor there is a lot more popcorn on the floor and it it is spread right across the screen.
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