In the junkyard, Captain Stottlemeyer shoots out a headlight in a Mercedes for Monk. While he is on the phone, Monk goes to examine the body and the headlight is intact again.
When Monk, Natalie and Disher talk to Gerald in the hospital, near the end of the conversation the hand that Gerald uses to hold the mouse changes between shots.
[38:30] Captain Stottlemeyer confronts his wife with (supposedly) the picture taken by Monk and Natalie which reveals Karen meeting another man. But the actual picture that he gives her and that she is holding is a shot of an empty restaurant, not the picture taken by Monk and Natalie.
The view out Gerald's windows in the hospital show several tall buildings, but there aren't any tall buildings near UCSF Medical Center at Mt. Zion.
When Stottlemeyer tells Monk he's already apologized twice and asks how many times he needs to apologize, Monk says "six." Stottlemeyer says "sorry, sorry, sorry" and then Monk is satisfied. However, this is a total of five "sorries" instead of six.
When Gerald complains about the last two pages being ripped from the book, he has at least a third of the book left to read.