From 31:06 until 31:13, the Native American Park Ranger is not cuffed, he is merely holding the cuffs in his hands. Later (31:37), he is properly cuffed. Presumably, this is for the actor's comfort.
After discovering the stone medicine wheel in the woods, Brennan takes a photo to send back to the lab. Booth, the Sheriff, and the Park Ranger are all standing inches from the wheel. However, back in the lab, the photo shows only the wheel; Booth, the Sheriff, and the Park Ranger are nowhere to be seen.
When Bones is photographing the arm bones, she arranges them in a silver tray. Later, when Zack and Angela are reviewing those photos, the bones are set against a blue background.
In the beginning, Bones brings a brown box with the severed hand to the shipping store to ship it back to her lab, then the next day, she brings in another brown box to ship, this time with the bear "doo-doo". It's the exact same box as the first clearly recognizable by the packing tape cut pattern.
Brennan is shown taking only a sample of the bear scat to send back to her lab. In order to properly assess the scat for evidence, she would have had to pick up all the bear scat, from every place the bear voided.
When Brennan and Rigby are examining the bodies in the autopsy room in Aurora, Brennan approaches the body of Ann Noise and as she turns away, recorder in hand, the 'corpse' can be seen breathing.
The park ranger isn't wearing the handcuffs, he's holding them in his fingers.
When Dr. Brennan, Special Agent Booth, and the Sheriff go searching in the forest in Washington State, there is a shot of Yosemite National Park's Half Dome geological formation, in California.
In the beginning of the episode, Booth tells Brennan that the hand was found in Eastern Washington. Later, Angela says, "What happens in Aurora, stays in Aurora." Aurora is in Western Washington, on the Olympic Peninsula.
The Flathead Indian Reservation is located in Montana, not in Washington State.
Hodgins talks about a Peruvian "soccer" team which crashes in the Andes in the 1970s, when in fact it was a Uruguayan rugby team
While examining the bear scat, Hodgins is wearing gloves as he should, but after finding an item he wishes a better look at, he grabs a magnifying light without removing the gloves, covering the light switch with feces. This could easily be transferred to other evidence, rendering them contaminated and possibly ruining a prosecution. A scientist of his caliber should know better.
When Bones collects the bear scat in the woods, she places it in a glass bowl. Much like a Pyrex food bowl, only she closes the lid with the gloved hand that was smeared in feces. A field scientist would never contaminate the collection kit with feces.
Both Bones and the local coroner pronounce the word "prion" wrong...it is properly spoken in the medical profession with a long "I" sound, just like the pronoun it represents. Poor script research.