Unfortunately optimizing combustion for fuel economy can increase emissions dramatically. Two primary examples- 1) efficiency rises with combustion temperature; however over a certain threshold temperature NOx starts to spontaneously form much more rapidly 2) efficiency rises with combustion pressure; however a high compression engine tends to have a combustion chamber shaped like a pancake instead of a sphere or cylinder, which tends to cause incomplete combustion raising particle emissions.

Edit: I forgot another, a leaner mixture (more air less fuel) helps get the most complete combustion for maximum efficiency and low particulate, but the more air in the chamber, the more free oxygen and nitrogen there is to form more NOx

Every engine strikes a balance between fuel economy, particulate, and NOx emissions. They are like the three corners of a project management triangle.