One of the clues is that the killer cannot turn their wrists, but when they are chasing the suspect near the trains, the killer is seen turning their wrists to hold onto the bars to get into the trains.
Booth states that Christopher Pelant used to communicate via flowers. Pelant only did that once and only after he learned that Angela and Brennan were doing so.
Dr Hodgins refers to the mold on the pizza and says it produces filaments (plural), which if you're cool you call hypha. The plural of that Latin word is hyphae, pronounced with a long a or e sound at the end. Anyone who has an advanced degree such as his should know the basics of proper biologic terminology.
When tracking the escape of the killer, Angela incorrectly pronounces Hagerstown, MD as "hag-erz-ton". The correct pronunciation is "hay-gerz-town".