Shifting Balance Theory
There are a number of different forces that affect evolutionary processes. Layman often think of natural selection as being the only force causing evolution but this is wrong. Genetic drift is another very important process that affect evolutionary process. Genetic drift refers to the random sampling of individual at one generation to build up the successive generation. The relative importance of drift to natural selection in driving evolution of a population depends on the effective population size. Have a look at Why is the strength of genetic drift inversely proportional to the population size?Why is the strength of genetic drift inversely proportional to the population size?. Genetic drift can typically randomly yield a population toward a fitness valley, from which natural selection will yield the population to either come back or start climbing the opposite fitness peak. This concept is called shifting balance theory. There has been a lot of work on shifting balance theory suggesting that it well be much more common than previously thought.
Phenotypic flexibility
One may wrongly assumed that if a mutation occurs to make, say, a bone a big longer, then one organism would simultaneously need mutations that would make muscles, nerves and other tissues longer accordingly. In reality our developmental process is very flexible to an environmental change or to a mutational change. This flexibility is very much used in medicine and agriculture. If a bone gets a bit longer, muscle might just stretch a little more and end up developing in accordance to the new mutation. It would therefore be wrong to assume that because we are made of a complex interaction of traits, that a mutation cannot bring anything that would not be beneficial. If you are interested in the evolution of complex system you might want to have a look at the post How did the cardiovascular system evolve?How did the cardiovascular system evolve? for example.