When the science dude takes a piece of the victim's hair, he examines it under a compound microscopic, but later when he reveals what he found in the microscope, he displays an electron microscopy image, which has a much higher resolution than compound microscopes.
While looking for the body of the victim, Brennan and Booth ask for help from Tutti and his handler. The dog playing Tutti is clearly a different animal than the one who played Tutti previously in, "The Man in the Wall" despite being the same handler/ cadaver dog pairing. In "The Man in the Wall" Tutti is brown. In this "The Body and the Bounty", Tutti is almost black.
The Emerald Ash Borer, while having a limited range, is not a rare insect.
In fact, it is a highly invasive species. Hodgins would have known his.
While tracking the moves of the injured fugitive, Sweets, Brennan and Booth all refer to Interstates as "the 66" and "the 81" whereas syntax on the East Coast refers to highways by number alone, as native Upstate New Yorker Boreanaz accidentally reveals when he says "The 66 to 81", reverting to the regional terminology he no doubt is used to hearing.