The vast majority of people have no problems with their wisdom teeth, whether they emerge or not. Impacted wisdom teeth are very common and are usually painless. They do, however, sometimes mess around with other teeth and throw off our bites (which will always readjust, not necessarily in a cosmetically pleasing manner, but the bite will adjust). Today, because we value straight teeth, impacted wisdom teeth are often removed prophyllactically, even if we have no proof that it/they will cause any problems.
Since impacted wisdom teeth are not evident until well after reproductive ability is attained, there is no reason to believe that malocclusion from wisdom teeth should be evolutionarily selected against. If problem teeth are so bad as to cause disability for an individual, that individual is removed from the gene pool.
Given two equivalent males, there's no reason not to entertain the notion that a female did not choose the one with better occlusion. So, it is theoretically possible that what we have now is an improvement over what was the state of our occlusions long ago. But there is rarely only one reason for two individuals to choose each other as partners, so... the teeth are relatively unimportant evolutionarily.
Or, if impacted wisdom teeth hurt enough to interfere with reproduction ("Not tonight, Og, I have a killer toothache.") the individuals who don't reproduce because of it will be dropped from the gene pool.
There may have been selection against wisdom teeth, because there are populations who have a lower incidence of third molars.
80% of all people will have problems with their backs at some point in their lifetime, which is a direct result of bipedalism in humans. You might ask why we became bipedal with that painful trade off. But bipedalism gave us some distinct advantages in survival. So did the expansion of our brains. The greater advantage has precedence in evolution.
Ancient Mutation Explains Missing Wisdom Teeth