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Perfect spheres only happen in mathematics, nothing is perfect in engineering.
Seriously though? Molecular imperfections in the alloy of the bomb case, picosecond timing differences in the explosive triggers used to fire it, varying density gradients in the explosive charges, the list goes on.
The regular shape of the divots on the outside of the sphere lead me to think they are likely locations where fuses or instrumentation were located. I am not certain if this is an implosion bomb, but that would look [like this](http://en.wikipedia.org/wiki/File:Trinity_Gadget.png).