First, there is need for care before considering the design in living things flawed.
I misunderstand what you mean by care; i do care?
Many such 'flaws' upon close examination are far from being such. For example, the human eye is a masterpiece of engineering that cannot be equaled by man's skills. If we humans cannot reproduce the eye or it's parts, it is a bit cheeky to proclaim it 'flawed'.
The first point here is very valid, we could find something that now we do not know or understand, the explains the illogical design or the world and universe (& life). But, most of the illogical design aspects can be logically explained using evolution, i.e. you are introducing two presumptions to get back to a logical explanation: the first, there is a designer, the second that he designed it to fit something currently not here.
On the next point. Although our eyes are quite adaptive, they are far from perfect. For each situation the human has designed an eye (i.e. camera) far better than our eye, if that be wide angle, resolution, distance, night vision.
I also ask why god gave everyone different eyesight? For example my eyes are far from what a camera can achieve. I have next to no night vision (i often use my camera to help me see in the dark), and if I don't use glasses i can't resolve anything past about 25cm. This is far from perfect.
There are about 1.2 million nerve fibres in our optic nerve. Most of these are used to link the cones in our foveae up to our brain to give us high acuity (still far from most cameras). And this high acuity area is actually very small, most of what we see is just fuzz (i.e. around the foveae), used for night vision.
The Bible does say that man was perfect before his sin. Sin brought with it a horrendous outcome to the human body, producing imperfection, sickness, and finally death. (Romans 5:12)
As i asked before, does this mean that before the original sin we were perfect, i.e. had different morphology (perfect). Then when the talking snake convinced them to eat the apple we metamorphosed into our imperfect selves.
Anyone who understands evolution would see that this was not the case.