The computer models they use are different so their estimates of value will differ. As a result, in one area Redfin will be higher for a specific house and Zillow will be higher in another. They are most accurate for homes that are cookie-cutter (like tract homes and condominiums). Neither is all that accurate for homes that are even slightly different from others in the area (such as remodeled or custom homes).
Also, neither Redfin nor Zillow take into consideration the condition of the home, the layout, landscaping or other intangibles that buyers base much of their value upon. This is why you need an experienced local real estate agent to more accurately determine what a house is worth at any particular point in time.