When Monk and Sally are fighting over the gum (the key piece of evidence in the crime), Monk is throwing Sally to the ground. In the next shot, she's throwing him to the ground.
In the scenes showing the double rainbow CGI, the colors in the upper (secondary) rainbow are in the wrong order. In a real secondary rainbow, the colors are always in the reverse order (with red on the bottom) from the primary rainbow.
A secondary rainbow is 1.8 times broader and correspondingly dimmer than the primary rainbow, not the same brightness and "40% smaller" (according to Monk, presumably referring to the narrower width) as depicted.
In the scene with the double rainbows, Natalie gets out of the car and points out the rainbows to Monk. Her shadow is clearly visible, and she is pointing in the approximate direction of the sun. Rainbows can only be seen when the viewer's back is to the sun, so she should have been pointing in the direction of her shadow. There would have been no rainbow visible in the direction Natalie was pointing.
The sky inside a primary rainbow is brighter than the sky outside of the bow, not the same as it is shown here.
Hypnosis is made to be a villain and it is an effective treatment modality. Dr. Bell states that hypnotism is no substitute for real treatment. However hypnosis has been considered real treatment since 1958.
When Monk is fighting Sally Larkin, in distant camera shots the fighters are obviously stunt doubles. The hair for both stunt doubles is very different.