This is the first time the title card for the show changed colors from red to blue and contained somber music.
When Castle and Beckett are looking for a cell phone signal in the freezer, Castle holds his iPhone from the top by the tips of his fingers. That particular model of the iPhone was notorious for dropped calls if you held it in the wrong place.
One of the terrorists has the first name Jack, his partner has the last name Bauer - a reference to Jack Bauer of the TV show 24 (2001). The two-part episode mirrors the basic concept of 24.