The three eyed alien is something of a science fiction cliché, but would an alien really have three eyes?
Without beating around the bush, the simple answer is maybe. That is to say, there is no reason an alien wouldn't have three eyes, so it is completely within the realm of possibility.
On Earth, most animal species have two eyes, but there are many creatures with multiple eyes too. Spiders, for example, as well as some insects and crustaceans. Strictly speaking, all vertebrates (animals that have a backbone) have only two eyes, but this is because of the particular path evolution has taken on our planet. While science fiction shows like Star Trek might tout the theory of parallel evolution to explain why all the aliens in the galaxy look like actors in wigs, it is likely that the course of evolution would be very different on an alien world. Not only would an evolving alien face different environmental challenges, but the chance mutations and random events that steer evolutionary changes would be somewhat different too. If a fish with three eyes happened to become the first to develop legs, then all the various creatures that followed would likely share the same trait. By the same token, aliens might not have evolved eyes at all.
The strange thing about nature, however, is that it does seem to prefer the symmetrical form. It's not often that you see a creature with three legs, for instance, or an ear on only one side of its head. Although this uniform symmetry may be a phenomenon unique to life on Earth; until we discover life elsewhere, we have no basis for comparison.
You also have to consider the practicality of having three eyes. Evolution tends to favor adaptations that are in some way functional. Accidental mutation or no accidental mutation, a trait will generally only make it past the audition stage if it contributes something to a creature's survival or reproduction. Having two eyes is clearly very useful; it gives us a sense of depth perception.
The only practical reason I can thing of for an alien having three eyes is the ability to see in another direction. If the eye were mounted on the top or back of the head, it might would be a useful lookout against predators. This would be particularly useful on a planet with low gravity, as predators are more likely to attack from above.
While there are no animal species on Earth with three functioning eyes, some fish and reptiles do have a small light-sensitive spot in the middle of the foreheads. This is known as a parietal eye, and is the closest thing to three eyes nature has provided. The most famous example of this is the tuatara, a species of lizard native to New Zealand. The tuatara's parietal eye has both a lense and a nerve connection to the brain, making it the most developed parietal eye in the world, but it cannot see as it is covered by scales. Everything suggests that this was once a fully functional third eye, but scientists have no idea how or why it evolved. Whatever the reason, this is proof that evolution can provide creatures of almost any configuration.