According to recent research, the London congestion charge did not improve air quality. Improved air quality was expected and previous studies found evidence supporting this claim. What this latest study does is highlight the complexity of transportation planning as quality of life issues are fighting with economic issues within the field. I suspect that mitigating congestion and environmental improvements are natural allies regardless of the results of this study.
I'm not sure why the air quality did not improve, but I would start looking for answers by examining the increase in the number of buses within the cordon. Perhaps an increase in transit use will have detrimental impacts on air quality. If so, that needs to be fixed, but it's not surprising.