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I've actually been polling co-workers who buy store eggs (I can't supply everyone at work unfortunately) and bought a few dozen myself to observe this phenomena. When my co-workers and I found plenty of fertile eggs (and it seems more often during the Spring and Winter) we started asking some chicken friends about this. My uncle asked around at coffee in Alabama. There is a guy in his breakfast group who owns a fairly large egg-producing chicken farm. He said that if he can't meet his egg quota to the distributor from his regular egglayer house, then he goes over to his hatching house and pulls some eggs layed that day to complete his order...thus, fertile eggs at the grocery. And like the rest of us (egg farmer to a lesser extent with light/temp controlled facility) his egg production dips in the Winter and he needs maximum reproduction of chicks in the Spring...so that's when he ends up pulling from the reproduction barn the most.
Anecdotal for me, but I have no other way to explain fertilized store bought eggs.
And for those buying eggs marked as fertile...over the years several of the kids at the school where I work have tried to hatch those eggs, even going as far as learning to read the codes so they get eggs layed within 3 days of purchase. Excellent luck with Trader Joe eggs. And absolutely, not one egg ever hatched from dozens of Whole Food eggs.