I think it's the airports. The plaza type pieces that act as the actual airport. They are all very close to eachother, which would explain the high contrast of pollution. I would try demolishing, and running the simulation for a while. I bet all my simoleans this is the cause.
EDIT:
Well I just watched the part in episode 54 where you demo everything... No dice huh? I'm stumped, unless it's coming from the closest connection? But pollution doesn't travel does it?