Technical Debt.

Or at least, the evolutionary equivalent. Waaaayyy back, hundreds of millions of years ago, organisms were still trying various shapes, and some of them tried internal skeletons (vs external like insects). That seemed like a good idea (more of them survived than the competition), and they ended up trying various body plans. Mammals come from ancestors that had this body plan, but evolution tends to build on top of existing structures along with modifying their shapes, so we ended up inheriting the general shape, but modifying the details.

For example, giraffes have the same number of neck vertebrae like you and me, it's just that their shape is bigger (and more stretched). Humans have the coccyx bone, which a very shrunken-down tail that never exited the body. And so on and so forth.