When Booth is going through the trash he puts an egg carton on the counter but in the next scene it is not there.
Near the end, Booth describes a Kukri knife as a popular choice of weapon in Afghanistan. The Kukri is actually the traditional weapon of Nepal, not Afghanistan.
Booth misidentifies the knife as a kukri.
Bones pronounces "Cro-Magnon" with a hard "g". This is incorrect (although common), and given Bones' proclivity for pronouncing non-English words as closely as possible to the original, it is unlike her to not use the French pronunciation.
Dr. Brennan says "brain fluid" when there's no such thing. She should have said cerebrospinal fluid.