According to "Affliction"/"Divergence" one Klingon colony world was infected with the Augment virus. Therefore both smooth and bumpy Klingons should have co-existed in the Empire, even though we never saw it on TV or film (this was, however, depicted in the post-series Enterprise novels and a few old TOS ones too)
In Into Darkness
we'll see about a dozen Klingons, but only 3 or 4 of them unmasked - and since what's under the masks of the others isn't revealed, some could very well be smooth-headed. So no continuity error, IMO.