When Brennan and Booth discuss the case at the diner the same extras walk past the window multiple times. Notably a large man in dark clothing crosses left to right twice.
Angela uses her rendering of the victim's face to check against missing persons' reports to find his identity. However, the victim was never reported as missing. His roommate was unaware he was missing. If someone else had reported the victim missing, the roommate would have been contacted as part of the investigation.
Angela states that it'll be hard for her to identify the victim "without eyes, ears, lips, or a nose." She's created facial reconstructions with only a skull before; having any flesh must make the task simpler.
During the talk with Hodgins at the end of the episode, Jessica says that she does not understand what 'Drosophila melanogaster' means. It is virtually impossible for anyone with any knowledge of natural sciences (Jessica hold a M.S. diploma at least) to not know the name of this insect as it is very commonly referenced throughout the learning materials and research papers.