In addition to the other points that have been made, it's worth noting that we live in different climates (some artificial) and eat a different diet (much of it artificial) than did our ancestors. (I don't know what the acne rate is among modern-day tribal societies.) Tens of thousands of years aren't enough to completely rewire hormonal effects on sebaceous glands in response to a rather minor selective effect.
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).