Well, some primates including humans have lost the ability (through genetic mutation) to synthesize vitamin C, while almost all other mammals can.
Not all vertebrates reproduce the same way; marsupials versus placentals.
There are also a great many sub-optimal design elements all around the animal kingdom. For starters, in humans we have poorly-designed spines and knees for upright locomotion, which is why back pain and knee injury is so prevalent.
We have a sharp ridge inside of our skulls which damages our brains very easily.
We have a (unique in nature) crossover food/air pipe construction in our throats which results in many choking deaths per year. It's benefit to the species (the ability to produce complex speech) far outweighs the cost to the species.
God is a pretty poor designer.