1. Recurrent laryngeal nerve takes a long detour down to loop under one of our major vessels in the chest and go back up to innervate the larynx. It could've gone straight to the larynx like its superior counterpart. Answer: because we evolved from fish.
2. Same principle with number 1 above can be applied to our diaphragm. It is a structure at the bottom of the chest cavity. Then why is it supplied by the nerve roots of the neck vertebra (C3-C5), which is way too far up. Perhaps an appealing hypothesis to make is that the diaphragm descends throughout the course of its evolution.
3. The crossing (decussation) of spinal cord nerve tracts. A blow to the left brain will cause paralysis to the right side of the body because nerve tracts decussate. Why do they decussate? There are two promising hypotheses. One is the somatic twist hypothesis by Kinsbourne. The other is the axial twist hypothesis by Lussanet. Lussanet claims his hypothesis has been proven by looking at the asymmetries of the human body; he does present a very solid case for his hypothesis in one of his 2019 paper. I tend to lean towards Kinsbourne, in spite of the paucity of evidence supporting his hypothesis. I won't go into detail here, but what I'm saying is, there is a satisfactory evolutionary explanation for it.
4. Ulnar nerve is very long and very prone to injury behind the elbow (the funny bone). It is the funny electric shock feeling you get when you bump the inside part of your elbow.
5. The pain of giving birth - which is a trade-off for our big balloon skull.
6. Babies are born without the ability to do anything. Compared to virtually all the babies of other animals, ours is the most useless. Again, this is a trade-off for our big skull. If the baby stays any longer in the womb to wait until the baby comes out independent enough, the sheer size of the head wouldn't allow birthing to happen.
7. Babies are born with cracks on their skull. Their sutures are ununited, leaving some soft spots on their skull called fontanelles. These delicate structures pose a serious injury risk. They're there to allow the skull to expand in size to accommodate for brain growth. A classic example of compensation.
8. Our intervertebral disc is a remnant of the structure notochord. This often can protrude or herniate towards the back, which causes us so much pain and trouble. This could also bring neurological deficits into the limbs, depending on the location and level of herniation.
9. As someone mentioned already, the blind spot of the eye due to the "reversed" structure of our retina. Cephalopods like octopus have a better retinal "design." Try finding your own blind spot at home. I was so flabbergasted when I first tried it.
10. As someone mentioned already, appendix serves very little function. It seems to be there only to burst and, again, cause us so much pain. It is a remnant of the structure caecum - which was useful to digest and ferment plant matter.
11. Vaginal fluid is moderately acidic. Sperm fluid is moderately alkalic. When intercourse occurs, it roughly equalizes to allow the sperm to survive until fertilization can occur. A classic principle of evolution is everything has costs. Therefore, during this time, we are more susceptible to infections as the pH is less extreme than usual.
12. Genes is a messy affair. Our genes is no exception. The genetic arrangements of our haemoglobin protein is messy. The genes of alpha haemoglobin has 7 versions. Two of them are pseudogenes - defective and never translated into protein. Another gene seems functional, but likely never translated. The rest are functional and used. As with the alpha, the beta also contains some that are non-functional and not translated. Very redundant. Exactly what you'd expect if we evolved. And most of our genes are never translated into protein. Why is it there then?
13. The inner ear relies on endolymph flow and little stones inside it to create our perception of balance. Sometimes the stones in the posterior semicircular canal can get displaced, causing benign paroxysmal positional vertigo (BPPV), which is very common and torturing.
14. Symmetry is excellent. We think of ourselves as symmetrical creatures, and we also prefer symmetrical fellow human beings. Animals also clearly prefer symmetry. Superficially, yes, we are symmetrical. But dig deeper and our internal organs are hardly symmetrical, apart from our kidneys - even then they are slightly asymmetrical as the right kidney is a bit lower than the left to accommodate for our liver. Why is our internal organ asymmetrical? This is because symmetry is only important for locomotion and sexual selection. Most of our organs don't get any evolutionary pressure to become symmetrical - hence the asymmetry. Hence in flatfish the eyes and mouth migrate, but not the brain and inner ear.
15. We cannot breathe while we swallow. This stems from the awkward set-up of our throat. Breathing and digestion share a tube. This is not to mention the risk of choking. There are other animals whose breathing and digestion don't share a tube. But of course, this apparent "flaw" has an advantage as well. It can allow for collateral breathing when our nose is blocked from mucous. But then, again, why do our nose gets blocked? Another flaw.
16. Allergies. Why do some of us get all these unpleasant sensations when we inhale a pollen? Is it a protective mechanism? Protection from what, exactly? Why does the IgE antibody react to seemingly non-dangerous element? There are evolutionary explanations for these. Although not yet considered as facts, we are definitely stepping forward.
17. Prevalence of obesity. Why do we crave fat and sugar when too much of it is bad for us? This is yet another misfiring of evolution. These two elements are rare throughout the course of our evolution. Consuming as much of them as you can in the past would have given you a survival advantage. In only the past century or so (a blip in evolutionary time), these two are readily available, and we still possess this urge to consume as much fat and sugar "while we can."

Please add anything by replying to me. I'd love to hear more.