There were some warning signs which hinted that VW was cheating in its emissions numbers. According to Automotive News today:

"A few years ago, engineers at a Detroit automaker tested and then took apart a diesel-powered Volkswagen Jetta, trying to figure out how the car could meet stringent U.S. environmental standards without an expensive selective catalytic reduction system to help neutralize its emissions.

They were flummoxed.

They couldn't duplicate the claimed EPA emissions test results on the road.

But that is as far as it went."