What's your favorite weird little detail from a movie or TV show that you only noticed after several viewings?
I was just thinking about this the other night. I couldn't sleep, so I fired up the first Hobbit movie and skipped ahead to the "Riddles in the Dark" scene. And I noticed that during the game, Howard Shore plays the "Pity of Gollum" cue from Fellowship of the Ring, which we haven't heard since the beginning of The Two Towers. By the end of that movie, the "Pity" theme has been effectively retired, replaced by "Gollum's Song," which is introduced at the end of Two Towers (as performed by Emilíana Torrini) and appears throughout Return of the King. But this version never appears in The Hobbit. That's because at this point, the characters really don't know that Gollum is a tragic figure and think of him as just some predatory cave-dwelling weirdo with a jewelry fetish. It's more appropriate to play the music we associated with him in Fellowship, before we learned his true nature.
It's not unusual for characters to develop a new theme song over time, either as a reflection of their development and growth, or because of an editorial decision or a new composer taking over. In the original Star Wars, Darth Vader and the Empire have a very different motif than the universally recognizable "Imperial March" from the other films. I was always sort of surprised this wasn't rescored for the SEs, since I remember hearing John Williams talk about it. But it's pretty sophisticated to go back and reuse themes that the audience might have forgotten about in the intervening years. And after rewatching bits of An Unexpected Journey I noticed a number of motifs from the LotR films, some of which only appeared once or twice, like the "Moria" theme that plays when Gandalf hands Thorin the key to Erebor. (I suspect also that Shore planted the seeds of the "Misty Mountain"/"Over Hill" theme in the cue that plays when Gandalf picks up the map in Bag End at the beginning of Fellowship. Now that's planning ahead.)