Perhaps the overall amount of general entropy can be be increased by isolated pockets of complexity, just as eddies and vortices forming in a stream can increase the overall flow, or at the very least, are an unavoidable consequence of that flow.

A plant growing in a barren field is an isolated pocket of complexity surrounded by low-order structure, but the plant breaks down soil and sunlight into simpler forms to nourish itself, thereby increasing the total entropy. Another example, closer to home, a complex civilization like ours appears to reverse entropy, but in order to keep it functioning and growing enormous amounts of hydrocarbons have to be burned down into simpler forms to provide the needed energy.

The appearance of complex structures and processes are not necessarily a violation of entropic flow, in fact, they may assist it. Highly complex forms break down lower complex forms in their environment, and the total entropy actually increases.