In the sequence where Clark apologizes for speaking out loud his thoughts on the relationship between Dr. Brennan and Booth, one shot, Angela is seen behind Dr. Brennan and beside Dr. Soroyan (behind the female skeleton), the next shot she is seen behind Clark (behind the male skeleton) who was facing Dr. Brennan.
When Booth, Brennan and Hannah meet at the Founding Fathers, Brennan asks Hannah to tell her how her and Booth met because he hasn't told her about it. This is inconsistent, because previously in The Mastodon in the Room (2010), Brennan actually asks Booth the same question and he tells her they met when he arrested Hannah for being in a restricted area. The story, however, changes in this scene when Hannah tells her that Booth had saved her life when an insurgent opened fire.
When Dr. Edison calls Dr. Brennan to tell her the commonality between the two victims, osteopenia, he mispronounces the word as "osteo pen EE a" instead of "osteo PEEN ee a" which rhymes with encyclopedia.