It could be that you're getting incomplete ignition, then the computer tries to tell the engine to compensate, still within norms enough to not throw a code, but changes something and causes it.
You're right, though, it's counter-intuitive to the norm.
More than anything, I've only ever noticed a slight reduction in mileage due to lack of complete combustion of higher-octane fuels in my cars that don't need it.
I’ve heard of excess carbon buildup from running higher octane fuel than needed.