[general_re]

It's not an optimal packing. So, were it designed, the design was not perfect, only good enough.

Is that because, as CobaltBlue suggests, it may have been constructed to conform to some external structure, or is it inherently sub-optimal?

[Doctor Stochastic]

It's inherent. The bees sometimes slip into the optimal packing for a few rows, but then they revert to the sub-optimal form. This happens in the wild or in hives.

Survival of the adequate.