One problem with the Atom Economy calculation is that it does not take into account the nature of the by-products. A reaction that generates tonnes of carbon dioxide presents a greater environmental problem than one that produces a lot of water.
It is sometimes helpful to consider the economy on the basis of the elements involved. Making maleic anhydride from benzene is used as an example.

In this case the problem is that 33% of the carbon available in the reactants is not incorporated into the desired product, but becomes carbon dioxide. Although the hydrogen and oxygen have a much lower atom efficiency, they are included in a much more benign product - water.