An important thing to realize is that evolution doesn't actually care or think. For a human, if a small change makes a significant difference in say, car safety, it's relatively easy for other humans to adopt this same change in all cars, and it quickly spreads. Evolution, on the other hand, can only effect gene pools through breeding rates and survival. An acne resistance gene might be all upside, but if people with zits still breed at the same or nearly the same rate as people without then it won't spread at anything like a noticeable rate.
This may be a question trivial for you, but: Why is there variation inside a species? On some instances, you could argue that the Nash equilibrum is mixed (for example, different men prefer different physical appearances of women, so women of different appearance can coexist), but: What the hell is the evolutionary advantage in having zits?
Probably, it has something to do with genes of different types (all of whom have a good reason to stay in the gene pool by a mixed Nash equilibrium) mixing up and producing zits, but: Why should evolution, that managed to create eyes and brains, be unable to get something against this working if other members of the same species can perfectly manage to avoid them? Because such a gene can easily exist in individuals that don't have that particular problem (and I can't think of any adverse effects this would have), it should be able to spread even if not all members of the species have a particular problem. The disturbing thing is that I imagine a working fix without adverse effects to require only pulling some hormonal levers, not coming up with the complication that is needed to make a proto-eye better by a positive amount (so that the mutation can survive).