I believe when people say it is perfectly designed, they are generally referring to the fact that it is perfectly designed to allow sustained life (unlike any other planet in our solar system).
Look at Earth, it is situated perfectly away from the sun. If we were further, it would be too cold. If we were closer, it would be too hot. If it spun faster, we would be in trouble, slower, and we would be in trouble still. We are the only known planet that has life in this gigantic universe.
In terms of species dying or going extinct. That doesn’t indicate a flawed design. All creatures that at some point existed, probably fulfilled their purpose for existing, whether it be balancing out the food chain, helping plants reproduce by spreading seeds, or providing some resource for man, or whatever.
And also, who is to say that the there never would have been extinction or death if there wasn’t disobedience in the garden? We don’t know that. It could have been designed perfectly, but after the fall God chose to let things happen as they did with our free will.