The cucumber is bitter? Then throw it out.
There are brambles in the path? Then go around them.
That's all you need to know. Nothing more. Don't demand to know "why such things exist." Anyone who understands the world will laugh at you, just as a carpenter would if you seemed shocked at finding sawdust in his workshop, or a shoemaker at scraps of leather left over from work.
Of course, they have a place to dispose of these; nature has no door to sweep things out of. But the wonderful thing about its workmanship is how, faced with that limitation, it takes everything within it that seems broken, old and useless, transforms it into itself, and makes new things from it. So that it doesn't need material from any outside source, or anywhere to dispose of what's left over. It relies on itself for all it needs: space, material, and labor.