After a few hours of working on this I will answer my own question, for posterity.
Apparently the Exit Cue, by default, is placed at the beginning of the file. This behavior was occurring because I had defined a 3 second fade-out and 3 second fade-in as the default transition. So upon playing a new track it will immediately arrive at the Exit Cue and begin its fade while also triggering the next one because it's set to infinite loop. With a 3 second fade out and fade in Wwise manages to amass 15 instances of this track :)
I would think that Exit Cues would default at the end of the file, not the beginning.