I had the exact same problem. In looking for a solution, I came across this forum post on Creative Cow, titled "Green squares on Premiere exports, CS6":https://forums.creativecow.net/thread/3/928886
Common factors in all people's experiences: color correction was performed and "Use Maximum Render Quality" was checked during export. So these two things seem to be triggering it.
While there is no explanation as to the cause, the solution worked for them and worked for me. Simply uncheck the "Use Maximum Render Quality" box in the export window.
Nice catch, James. We debated this piece of explanation, but ended up saying it this way because conceptually it makes it easier to grasp negative fill this way. Blue wall reflects blue. Dark brown wall reflects dark brown. Black wall "reflects" black.
My analogy with people is that if you look into a mirror and see a black object, you say the black object is being reflected in the mirror. However, technically speaking (as you point out) it isn't. In fact, a person could argue that everything in the mirror is reflecting EXCEPT FOR the black object. ;)
A physicist would parse it out and want to get into interference patterns as the lightwaves move by a barrier (the flag), reflectance values of surfaces, spectral analysis of the reflecting light, blah, blah, blah. ;) That wasn't our goal. We hope this generalization in our approach and teaching added understanding and didn't confuse people more.