There are many reasons why natural selection may not produce a “perfectly-engineered” trait. For example, you might imagine that cheetahs would be more fit (produce more offspring) if they could run just a little faster and catch more prey. Here are a few reasons why natural selection might not produce perfection or faster cheetahs:

• Lack of necessary genetic variation
  Selection can only operate on the available genetic variation. A cheetah might run faster if it had “faster genes” — but if “faster” genes are not in the population from mutation or gene flow, evolution in this direction will not happen. A “faster” cheetah might evolve if the fastest cheetah in this population passed its “faster” genes to its offspring.

• Constraints due to history
  Perhaps a different arrangement of leg muscles and bones would produce cheetahs that run faster — however, the basic body form of mammals is already laid out in their genes and development in such a mutually constrained way, that it is unlikely to be altered. There really may be “no way to get there from here.”
• Trade-offs
  Changing one feature for the better might change another for the worse. Perhaps “faster genes” are in the population — but there is a trade-off associated with them: running faster for short distances means the cheetah’s metabolism requires even more energy or that the cheetah’s legs must become hazardously delicate. Although longer limb bones increase stride, their chances of failing due to bending loads increases as well. In this case, perhaps it would get no net increase in fitness as a result of the “faster genes.”