Air pollution in Simcity seems to come from nowhere

In previous SimCity games, pollution sources would be placed at the map edge to limit the area affected by the pollution. This time around, in addition to the normal air pollution of the building, there is a regional pollution level. Regional pollution drifts in with the wind. If your region has a high amount of polluting buildings, you will still get some regional pollution - that's normal.

There was a bug in patch 2.0

It was fixed in patch 3.0 on 2013-05-08

Air Pollution: Fixed more issues where cities that placed air polluting buildings received large amounts of air pollution from unknown sources.

The bug in patch 2.0 was that a very low number of polluting buildings could cause massive regional pollution. I played one city where 4 low density industry buildings caused so much regional pollution that the germ map was fully lit up and two (maxed) clinics couldn't keep up with the death.