In the diner scene with Angela talking to Gordon Wyatt, she told him that in order to be able to successfully eat the sandwich he was wrestling with, he'd have to distend his jaw like an articulated python. This should have been a reticulated python.
In season 4 Booth's brain tumor is diagnosed as a cerebellar pilocytic astrocytoma; however in this episode, when Booth thinks his marksmanship may have been affected by the brain tumor, Bones tells him it's unlikely because his tumor wasn't cerebellar. She says the tumor was in the tempero-parietal region. While it is possible his initial diagnosis was incorrect (this was not addressed on the show) it is highly unlikely that these two regions of the brain would be confused on a CAT scan.
The rusty gun that was referred to as a Ruger Mark III and was buried for 20 years is impossible became the Mark III was first manufactured in 2004 and the show first aired in 2009. Even in real time it isn't possible because the Mark III hasn't been around for 20 years.