Great question — answering as the UphillTech team:
I'm not 100% sure on why this happened, but I know what those "craters" are. They are where there have been bubbles of gas (likely air) definitely under the shell, but possibly under the membrane too. I see things like this on a regular basis in agar plates used for microbiology. There could be two causes of this that I can think of: A minor leak in the shell, maybe not visible to the naked eye, but enough that when the eggs were lowered into the boiling water, the gas expanded and bubbled away from the gas entry site. If you look closely and rotate the egg you may be able to see a higher concentration of craters nearest where the entry was. You may have seen a trail of bubbles coming off...
Full answer by bob1: https://cooking.stackexchange.com/a/116188 (CC BY-SA 4.0).
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