Not every trait necessarily confers a specific evolutionary advantage. Some traits may exist as side effects of other traits that do confer an advantage, or they simply may not confer enough of a disadvantage to have been bred out of the population.
Severe acne can run in families, but in general, zits are the result of pores being blocked so that the oils released by sebaceous glands build up. I doubt there is a specific gene or set of genes that causes all pimple formation. One's susceptibility is probably increased by genes that influence one of the factors in the formation of zits, if the heritability is genetic in origin. In general, though, they seem to be just a relatively minor (although irritating) malfunction of the dermal system.
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).