During the scuffle on the roof, Natalie's shoes are kicked off and then re-appear and disappear through the remainder of the scene.
Near the end when Joey is with Harold in the hall before going to the roof, there is a partial shoulder of the man coming out of the lift before the lift's doors are open.
When Joey and Harold Krenshaw are talking to the woman and the two children about the picture they made for Harold, Joey grabs the picture and the marker from Harold to give the picture back to the children. After he hands the picture to the children, Joey grabs the marker from Harold for a second time.
The gun falls out of Joey Krenshaw's hand onto the ground twice.
The burned car in the beginning is a 2000-2005 Chevrolet Impala, which were manufactured in Ontario, Canada. The VIN that is later recovered starts with TPL, which would be from a car built in the Czech Republic.
Even back in the early 2000s, law enforcement agencies would have had instant access to VIN information. Lt. Disher would not have been waiting for a phone call to tell him who owned the car. As soon as he made the request he would have had the information.
During the fight on the roof near the end of the show, and then after the fight right after Harold appears to fall off the roof, a windsock can be seen fully extended as if the wind is blowing strong, but Natalie's hair is not moving at all.
Obvious stunt double for Natalie when she and Monk are fighting Joey Krenshaw on the roof.
In the distant shot of Monk and Natalie on the roof after Harold "falls off the building" the wall at the building's edge is visible, and it is a good 3 feet from the elevated platform that Harold fell off of.
The burned car in the beginning is a 2000-2005 Chevrolet Impala. The headlight switch shown is from 1970s-1980s vintage car.
The shot of the apartment row, depicting the exterior of Victor Grajna's apartment, is old file footage of a Manhattan street, where you can also see World Trade Center Tower 1 (North Tower), which was destroyed six years earlier.
The story is set in San Francisco, but during the rooftop fight scene, as Natalie runs in to deliver the first blow, the downtown Los Angeles skyline is clearly visible.
When Natalie and Mr. Monk are in the waiting room, Natalie is holding a magazine with the Frisco Fly on the cover. It's clear that it is Harold, in costume, on the cover of the magazine. Harold had not yet had interviews and then named the Frisco Fly and no one knew the true identity of the real Frisco Fly yet.
One of Mr. Monk's many phobias is riding in an elevator, yet he gets into an elevator with no problem at the hospital after visiting Harold. Later in the same episode he mentions how difficult it was for him to ride an elevator to the roof.
When Natalie and Monk are on the roof after Harold fell, Natalie finds Harold's glasses in the middle of the roof, nowhere near where he fell off. Monk should have recognized that Harold never got to the top and couldn't have lost his glasses in the middle of the roof.