Was playing a random map in the Simulacrum, I noticed that the music would randomly change tracks.
It might be in issue with how long the game was running. I know I was called away a lot so I had to pause often.
Beyond that, I can't see any pattern there might be to help debug this.
I don't have much to contribute here other than the fact that I've had this happen as well. It has definitely never happened on the story missions, though I can't remember whether it happened in Inception or the Exchange. While I can't say with 100% certainty, I believe it skipped at the same spot both times I heard it do so.
I also had this happen when i was editing some of my maps! One of the songs was about to go to the violin part, but it just skipped it and went to the next song.