When Booth and Bones are driving right after they id the skull Booth's hand changes places multiple times. Sometimes it is near his head and once it was on the steering wheel, he also puts his sunglasses on his forehead yet in the next scene they are now covering his eyes again.
Hodgins is looking at photographs of Angela's vacation on a screen. The photos are different when viewed from over Brennan's shoulder, to the closer shot of looking over Hodgins' shoulder.
When they are looking for blood on the humvees hood booth does not have his flashlight out but when they find some all of a sudden he does.
When Bones, Booth and Angela are out in the middle of the desert supposedly five hours from the town and five days from the near highway there's a shot where you can see a car driving in the distance behind them. They're supposed to be in the middle of nowhere.
When Brennan first arrives in the desert, she and Angela are traveling in a Jeep Wrangler. The radio which is shown when Brennan attempts to tune the station (to no avail) is actually that of a Ford Mustang. The oval "FORD" logo is visible on the right side of the cassette-flap.
When the sheriff takes them out and they find the rock formation and they turn off you can see the tire tracks from previous takes.
During a scene where Booth and Bones are driving through the desert, near the beginning of the episode; a mountain suddenly 'appears' in the background over Booths' shoulder.
Peyote does not grow in northern New Mexico on or near the Navajo Reservation, but is only found in areas closer to the Mexico border in southern AZ, NM, TX.
The setting of the film is supposed to be northern New Mexico based on the indication that Bones flew into Santa Fe, the mountains of Taos are used in scenery, the Sherrif refers to "Otero Canyon" and the proximity to the Navajo Reservation. However repeatedly in their search for the missing party, several cast members indicate that "Mexico is 80 miles that way" (south) meaning they would be closer to Las Cruces.
Saguaro cacti do not grow on or near the Navajo Reservation. Saguaros are indigenous to the Sonoran Desert of Southern Arizona and New Mexico.