There is no good reason, from everything science tells us, why the human body shouldn’t be perfect. The scientific model builds Nature up from the simplest, smallest components to the largest and most complex. There is no doubt that at the smallest scale subatomic particles, atoms and molecules, and are perfect, because they have endured without change for billions of years.
Did imperfections arise with the beginning of life on Earth? Single-cell microorganisms are thousands, perhaps millions, of times larger and more complex than the smallest molecules that they are built from. But one-celled creatures have endured for something like 3.5 billion years. Since they reproduce by cell division, the most ancient forms of amoebas, algae, protists, and so on are actually still with us–literally the first amoeba has never died or aged. Life forms with complex structures constitute much less than one percent of living things; a bucket of ocean water is likely to contain hundreds of unknown variations on their DNA.
Imperfection gained the stage thanks to the same force that produced perfection: evolution. We suffer from disease, resist ageing, and fear death, but all of these are creative steps as far as evolution is concerned, since evolution triumphs through maximum diversity and an endless supply of new genes leading to improvements.