(At 36:10 and 36:29) Henry Spencer is seen behind Chief Vick, Shawn and Gus, but doesn't enter the scene until later (at around 21 mins)
The first two numbers we see Gus punch into the lock is 7 twice, and the last number he punches is in the top row. Later he says the combination is 25329, and 9 is in the bottom row. Also the green light on the lock lights when Gus unlocks it, but doesn't when Shawn unlocks it.
When in the morgue while Shawn is wearing the dinosaur head, the width of the open mouth of the head changes throughout the scene.
While parking in front of a gate of the Deacon Walker Farms, you can perfectly see between shots Gus isn't wearing a seatbelt, then he is, then he isn't again, then finally he is when he leaves the car.
The teeth on young Gus's dinosaur head change size and position depending on whether the shot is from inside or outside the head.
A numeric keypad lock like the one on the garage door wouldn't make a "second click"; that is only found in a mechanical dial combination lock.
Jules comforts Lassiter by citing Lou Boudreau ending Joe DiMaggio's hitting streak. Actually, it was the play of Indians' third baseman Ken Keltner who robbed Dimaggio of two hits in his first hitless game in two months.
Gus is wrong when he says trilobites are fossil fish. They are fossil invertebrates.
When it is mentioned that Farmer Shooty Pants was digging to try to find where he buried his business partner years prior, Gus says the holes near the house were dug with a bulldozer. Bulldozers don't dig they move materials (soil, sand, gravel, et al). To dig holes one would need a backhoe. While one is never shown, it's possible that Walker had a backhoe attachment for his tractor, but he definitely didn't dig any holes with a bulldozer.
The curtains in Henry's house switch windows when he is lecturing Shawn and Gus. There is a set of plaid curtains and a set of purple curtains that switch windows depending on whether it is a long shot or a close shot.
While at the farm, both Shawn and Gus refer to the backhoe as a bulldozer.
The lock behind the keypad on the Professor's garage is a deadbolt, which would not work on a sliding door.
While Gus is digging and Shawn is relaxing on his back, James Roday Rodriguez is clearly expecting the shovel to land on him and braces for the possibility of it hitting him in the face.
When Shawn and Gus are investigating the shed, Shawn sees a box of fruit from Ojai, CA. He asks, "why would someone frequent a fruit stand that's over 50 miles away?" In reality, Ojai is approximately 35 miles away from Santa Barbara.
Franzen's department at the university is first said to be paleontology, then later anthropology. Also, anthropology is the study of humans in the past and present, not dinosaurs.
Gus made the dinosaur head for "Stone Age Day" at his school. The Stone Age happened during the time of early humans, long after dinosaurs were extinct.