On latest test build, B587Unstable, CTRL+S x2. Roughly three out of ten sets will produce the reported error.
Replace the second CTRL+S with escape, F5 or CTRL+O and this error will be produced with the above odds.
CTRL+S repeatedly at roughly twice per second does not seem to produce the error.
Speed it up a bit, four times a second, and you begin to get the errors. But no one should be saving this fast, anyway...
It's just bad luck. And if you get it, after you save and quickly go to F5, Escape or CTRL+O, you'll get the error.
Granted I made no changes when I did this, but I tried for a very long time to do CTRL+S -> CTRL+O without any error. Perhaps a different story if something new is changed.
Actually... I just reproduced it. What I did was added a single beat, saved and about half a second later, your preferred action. (Escape, CTRL+S, CTRL+O, F5.) Then removed the beat, save, action. Out of ten tries using the above method, sets 2, 3, 5, and 10 produced the error.