Shawn, Gus and Scott go to Waring's office to investigate the shooting that occurred there. His office is on the second floor of the warehouse and has windows. Shawn even opens them to determine where the bullet may have gone. Yet when they go outside to search for the bullet, the warehouse is shown behind them and it is only one story tall and there are no windows visible.
When Shawn and Gus are looking for a bullet that had been shot into a tree five years earlier, Gus suggests Shawn is looking too low because "trees grow." In fact, trees grow vertically by adding new cells at the top of the tree. They will add rings and get wider around the trunk, but a bullet in a tree would be at the same height five years later as the day it was shot.
The chrome on the motorcycle as Shawn is running towards it doesn't reflect what it's supposed to.
The trains seen in the episode are not Amtrak trains but rather VIA Rail trains (the passenger rail provider for Canada). VIA Rail does not operate in California or anywhere in the United States.
The train station depicted as Los Angeles Union Station is really the Pacific Central Station in Vancouver, BC.
After the fight between Shawn and Federal Marshal Daniel Wayne, Wayne goes around his car to retrieve his gun, the boom is reflected on the car.