When Daniel Carder first saw emissions abnormalities while testing Volkswagen vehicles, he thought, "What have we done wrong?"
After checking multiple times, Carder's research team at West Virginia University found early evidence that the world's second-largest automaker may have cheated on U.S. emissions tests. When the study ended in 2013, they publicly reported the findings.
"That was the end of our job," Carder, interim director of West Virginia University's Center for Alternative Fuels, Engines and Emissions, said Thursday on CNBC's "Power Lunch."
More than two years later, the alleged use of software in diesel vehicles to alter their performance on environmental tests threatens Volkswagen's reputation and bottom line. It has spawned broader scrutiny about how automakers worldwide handle emissions standards.
Volkswagen CEO Martin Winterkorn stepped down Wednesday, saying he was "stunned that misconduct at such a scale was possible" at the company. It is expected to name Matthias Mueller, CEO of Volkswagen subsidiary Porsche, its next chief at a meeting Friday, sources told CNBC.
Read MoreMartin Winterkorn resigns as Volkswagen CEO
When researchers like Carder report emissions problems, it usually ends with a voluntary recall under an agreement between the manufacturer and a regulatory agency, he said. It is currently unclear whether Winterkorn or other senior leadership knew about the alleged cheating, and Carder declined to speculate on whether it was an institutional problem.
However, he noted that, based on past experiences with similar issues, he would not sell a Volkswagen car yet if he owned one.
Read MoreEurope's carmakers caught up in VW storm
—Reuters contributed to this report