There are several different criteria you might want to optimize for that result in hexagons, not just close-packing of circles. (Obviously they are somewhat related, but if you step up to 3 dimensions then you start getting different shapes/structures for different criteria, such as a diamond lattice, an FCC lattice (voronoi cells make a tiling by rhombic dodecahedra), a tiling by truncated octahedra, ....)

In particular, bees probably make hexagons because that minimizes the amount of wall you need per area, for a given cell size. If bees were really just making something like a voronoi diagram from somewhat spread out points, you wouldn’t get quite so regular a hexagonal tiling.

I imagine there’s some research about the precise method by which bees build their honeycombs, if anyone wants to go dive into the literature.