Wow. For the first time in 10 years, I had this bug happen to me today, and it was a 6 song project like the one in your picture.
I think I might know the problem. Did this project contain a file with a really short file name?
Today I had a file that was mistakenly just named:
r.wav
And when I did my usual thing, the files ended up on more than two tracks like your picture. When I went back and correctly named the file from r.wav to a longer and correct name, the problem went away.