Denis O'Hare who plays Father Chris Shea here also played a character named Father Shea in an 2008 episode of Law & Order: Criminal Intent called "Last Rites."
Peter Gerety who plays Judge Harrison also portrayed Judge Daniel Phelan on HBO's The Wire.
In the scene where they are discussing Father Shea's background, Det. Amaro mentions in passing that Father Shea was a prison chaplain. This is a reference to Last Rites (2008) in which his character, Father Shea, also appears.
Denis O'Hare has had two different roles over the course of the series: *Episode 1.16 The Third Guy (2000) - Jimmy Walp *Episode 14.10 Presumed Guilty (2013) - Father Chris Shea
Det. Amara (Danny Pino) says "Did you hear anyone call you names, maybe Chomo, short eyes?". "Short Eyes" is old school prison slang for a child molester. The term originated in the late 1970s when Miguel Piñero adapted his play Short Eyes (1974) into a movie. The film is about a pedophile, or "short eyes", who gets tortured and ultimately killed by his fellow inmates after they find out what he is in jail for. "Chomo" is another, more frequently used, prison term used for child molester.