When the detectives stop their car outside the abandoned church, there is a shot of Rust looking at the horizon when suddenly a group of black birds take flight from the bushes. As the old Rust voices over the scene, the group of birds start making random patterns in the sky, one of which is the spiral sign as seen tattooed on the murdered victims' backs.
The two bible verses that Cohle quotes to Gilbough and Papania are 1 Corinthians 12:14 and 1 Corinthians 12:20.
The three flags seen along the wall in Major Quesada's office are: The U.S. flag, the flag of Louisiana, and the flag of Acadiana aka the Cajun flag. The latter is represents the Acadian (Cajun) ethnic group in southwestern Louisiana.