Okay, I've been playing through the latest commit as of this writing, and I'm about an hour and a half in, story-wise (just hit South Figaro for the first time).
So far, there is at least one consistent instance where the wrong track plays - when the cutscene with the Matron in Figaro Castle where you choose Sabin's name finishes, the music is supposed to revert to the "Figaro Castle" theme.
Instead, it reverts to the Opening theme. I have the in-game hooks disabled for the time being, as they cause known issues, and I'm trying to avoid issues that crop up where they might be the root cause, so I'm wondering if this is part of the "Track 0" issue. I will be on the lookout for more reproducible problems of this nature, so if this is determined to be an instance-by-instance problem, there will be a roadmap of places to look. Hopefully, this is merely a small symptom of a broader issue, so that fixing that issue will also fix this.