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This is one possibility, I've experienced it.  It was one specific hen. 

The poop and an egg come out of the same place, the vent, but travel through two different internal plumbing systems.  To keep the egg clean, a small bit of the egg-side plumbing sticks out maybe 1/2" or so to close off the poop side as the egg is laid.  For the vast majority of the hens this works great but like everything else to do with living animals occasionally something does not work as it should. 

I don't know for sure that this is your problem but it was with one of my hens.