Why do you think nature is perfect? I.e. what is your "gold standard" against which you measure?
Something that immediately comes to mind for me is all the death and suffering that is abundant through nature. If the only thing that matters is propagation of life, then nature does seem pretty good at it, but as a being that operates some layers above the selfish gene, it seems far from perfect.
What if this is the best it can do with all the things that can go wrong or are going wrong. Perfection does not mean things will never go wrong. They can and they will. I can give you example of process that is near perfection: photosynthesis. Nature can store energy and then utilize it without creating adverse effect on other life. This is just one example but there are many processes like this.
Wow we have completely different world views. I think nature is perfect and it's us who have gone too far away from it to notice and hence we are far from perfection as well. Ideally we should not be comparing us to nature since we are part of it. But somewhere deep down we know we are not aligned with it so we end up comparing it to humans which seems pretty grandiose on our end.