When the Captain is at the tombstone of Darren Leveroni, it states that he lived from 1980 - 1997. When the confession letter is read from the time capsule at the end, the accident happened on December 2, 1998.
When Monk returns home from shopping and finds the Captain making a sandwich, the kitchen island is missing.
When Leland is sitting on Monk's couch holding a glass of beer, the amount of beer changes. It is at a higher level, then a lower level, and then a higher level again.
At the end, Captain Stottlemeyer asks Karen if the letter she put in the time capsule is about him, but 10 seconds before this, you can see the letter clearly starts "Dear Leland".
Stottlemeyer read the note that his wife wrote and asks her "Is it about me?" But it was headed "Dear Leland" (his given name) so it was obviously to and about him.
When the gravedigger discusses Darren Leveroni's grave, he states that the ground was frozen solid. The air rarely reaches freezing in San Francisco. The ground never does.
When Stottlemeyer rewinds the videotape, the dialogue is heard in reverse (confirmed in the subtitles). VCRs can't do that. In fast forward or rewind, there is no audio.
When they are at the grave, the Golden Gate Bridge is visible and close. Further, the bay is to the right, placing them to the south of the Golden Gate Bridge. This places them inside San Francisco. However, no one has been buried in San Francisco since 1902.
[18:20], Karen Stottylmeyer says she's doing Bikram yoga. Bikram yoga is a proprietary form of yoga that requires a temperature of 105° F with a humidity level of 40%. There's no steam in the room, and Karen shows no signs of perspiration, which indicates that she's not doing Bikram yoga but instead doing regular yoga.