It's illegal, right? They were not supposed to use a first-season cue in the third season, without paying for a recording session to re-record it as a library cue.
I don't know if "illegal" is the word. It's a matter of the studio's agreements with the musicians' union, so I'd figure it's more a breach of contract than a criminal act.
But it wouldn't have been the first time TOS made end runs around the rules to save money -- like getting Wah Chang to build the communicator and phaser props as "study models."
I'm surprised. I thought we were getting performance takes, rather than creations of the music editor, with the exception of things like the cello-sweetened Death of Miramanee. My assumption with "joined" cues was that they were performed that way, almost like when you see pics of the Warner Brothers orchestra performing with Bugs Bunny up on the overhead screen. The orchestra & conductor are self-editing or self-syncing the cues, so they line up with the action (except for library versions).
Well, a lot of the cues we hear onscreen in a movie or show are edited together from parts of two or more different takes of the same cue. If, say, the first half of one take sounded better but the second half of a different take sounded better, the music editor could've mixed and matched to get the best version of the cue overall. So even a single isolated cue doesn't necessarily represent a single unedited performance. If you look at the reference numbers after the cue titles, sometimes one cue will be listed by two numbers or a range of numbers.
And it's worth pointing out that blending separate cues on a track so that the end note of one cue fades into the first note of the next is far from an unprecedented practice in soundtrack albums. It's often done intentionally to create the impression of a "suite," a continuous piece of music. It's not what I would've preferred here, but it's hardly a shocking departure from soundtrack-album practice.