An uplist of human 'design' flaws - or rather, evolutionary mishaps.
Wisdom teeth (already noted) with secondary abscesses, occasionally dissecting up into the cranium -> brain abscess, meningitis, epidural empyema.
Female pelvis too small for the human baby's head making birth difficult and prone to perinatal injuries to the baby.
Retinal arteries/veins lying on and in front of the retina of the eyes. Many causes of blindness come from this defective design.
Human wrist must extend to provide maximum finger flexing; a major human task is to hold things in our hands. So the wrist flexes a thousand times a day. Problem is that the median nerve runs through a bony trough covered by tough ligaments, the Carpal Tunnel. With every wrist flexing the median nerve is pulled in and out of that canal. The canal is easily narrowed by minor injuries or repetitive use. The nerve is injured causing pain, finger numbness, and weakness in thumb opposition.
Our abdomen. It houses our stomach, our liver, our spleen, great vessels (aorta) small bowel, and colon. In quadrupeds it is underneath. An attacker cannot easily get to it. The predator has to attack the tougher back and spine. But in the human the belly is sticking out there for some clawed or toothed predator or knife wielding human criminal to take a swipe and eviscerate us.
We can't transform uric acid into allantoin. It makes us vulnerable to gout.
Our enzymes that synthetise ascorbic ascid (vitamin C) are not created (but the genes are in our genome), making us vulnerable to scurvy.
Larynx too highly placed, leading to common choking deaths.
A bony projection, called the Odontoid Process, an extension of the C2 vertebral body lie a long finger, up to the end of the brainstem. It can easily fracture, especially in rheumatoid arthritis. That leads to death or paralysis of all extremities and inability to breathe without a mechanical ventilator. A simpler rotatory ball-socket joint would be better and safer.
Semi-soft disc material between vertebrae and just anterior to the spinal cord, were suited well to quadrupeds. But in humans the upper body weight compresses these and can cause herniation's with mild to moderate trauma. There are 6 of these (none at C1-2) in the neck, 12 in the thoracic spine, 5 (rarely 6) in the Lumbar spine. That is 23 flaws or accidents waiting to happen.
Hip joints perfectly suited to support human weight if there were four of them or 4 supporting limbs. In a biped, the stress causes extremely common hip degeneration, femoral neck fractures in women and older people. How often do you hear of that in a dog or horse?
Knees similarly are not strong enough with the tibial cartilage in two legs for human weight, jumping down, and running. If we had 4 legs it would not be so bad. How often do you see cats with knee problems?
Foot and ankle bones are badly designed. Most quadrupeds walk on their toes or the balls of the feet. This puts more weight on flexible tendons, ligaments and several bending joints spreading the stress. In the human food, we are walking on essentially our leg "wrists" and balls of the foot with an arch that is traumatized by walking and standing. When it falls it has an additional problem of severe foot pain. (see 10).
In those fallen arches, the plantar nerves are badly placed. Instead of weaving between or over top of bones to their skin sensory receptors, these course "under" the ankle bones, under the arch to the metatarsal joints. When the arch slowly gives way it stretches those nerves and eventually compresses them. This never happens in dogs or cats.
The Elbow flexes and extends, but an important nerve, the Ulnar Nerve mostly motor to the muscles of the forearm and hand. It unfortunately does not go in front of the elbow in the safer soft tissue. It courses behind the elbow which is fine in horses, but human flex the arm at the elbow that pulls and stretches the ulnar nerve in a long course behind the elbow in an "ulnar groove" and additionally a human sitting often rest elbows on a table, and that compresses the ulnar nerve. Dogs and cats don't do that.
The Brachial Plexus is a cluster of the nerves to the arm that travels through a triangle with the first rib being the bottom, the collar bone in front, and the scalene muscles behind. Also in the triangle is the brachial artery to supply blood to the arm. Poor posture, hanging by exercise bars from the hands, or throwing balls, cause the triangle to compress either or both structures. This is Thoracic Outlet Syndrome, the Neuronal form when the plexus is injured and vascular form when the brachial circulation is impaired.
Female urinary opening (urethra), vagina, and rectum all located in a close row so that rectal infection of the urethra/bladder/kidneys, or the vagina is risky. The old joke is why is the recreational park located at the sewage outflow pipes?
Appendix is a seemingly useless relic of evolution that often gets infected and ruptures in a life threatening peritonitis unless removed quickly. A few postulate that it's a kind of "backup drive" for our intestinal flora. If you have an infection so bad that your body needs to get everything out of there the appendix puts back what you need to survive. Obviously, this is less common than it once was.
Large veins in the legs, progressively dilating from standing, walking, run the risk of blood clotting when the human sits for a period of time. These veins send those clots north to the heart's right ventricle and directly into the lungs causing pulmonary embolism (clots and lung infarction) that is often fatal.) Quadruped animals rarely die of this. Many humans do.
Venous Cavernous Sinuses at the skull base on left and right are large draining veins from the brain. But inside of the vein there is the carotid artery taking blood into the brain, and several important nerves: III, IV, VI that control all eye movements, papillary diameter, and lens focusing, and V-1, V-2, and V-3 that supply sensation to the eye and face. This venous structure packed with these important structures is infected by sinus infection or pustules in or on the nose. Infection causes the blood to clot (thrombosis) that injures the nerves, makes the eye bulge and swell, and can cause spreading thrombosis into the brain which can be rapidly fatal.
Other cranial sinuses such as the transverse are located next to the middle ear that frequently gets infected in kids. The infection spread to the venous sinus and causes thrombophlebitis, the major effect is increased fluid pressure in the brain, venous strokes, and seizures. If all of those venous drainage pipes were internally situated, there would not be such a risk. (17 and 18).
Congenital birth defects caused by structures found only in primitive animals (but still in our genes): gills in our embryonic stage may have some left over at birth and a baby may have a partial gill (technically called a branchial cleft cyst.) These can cause pain as the person grows, or develop abscesses. Another is a chordoma, tumor composed of notochord tissue only otherwise found in ancient animals like Pikaea and Amphioxus. It preceded the evolution of the bony spine. We have one in our early embryo stages but absorb it. Sometime absorption is incomplete and notochord tissue grows (tumor) unfortunately in the clivus at the base of the brain.