You are absolutely right that the fuel economy numbers published by the Environmental Protection Agency, which appear on new-car window stickers, are the result of standardized testing, but there are issues that can lead to different estimates. This happened with Ford as you mentioned and, earlier in the year, with Hyundai and its sister brand Kia.
In Ford's case, it relied on actual tests conducted on another vehicle that is considered to be in the same vehicle family because it shares the same powertrain and other components. It then used a mathematical calculation based on those actual tests to calculate the numbers it submitted to the EPA -- all of which was acceptable in the EPA's eyes.
For fuel economy estimates on the Ford C-Max Hybrid, the company had used the Fusion Hybrid. After it met some criticism, Ford conducted additional testing and dropped the fuel economy estimate by 4 miles per gallon to 43 mpg in combined city and highway driving.
In Hyundai's case (which encompassed numerous models of the Hyundai and Kia brands), there was a procedural error during part of the EPA test that the automaker conducted at its testing facility in Korea.
The problem in both instances is that the EPA requires automakers to conduct their own fuel economy tests and submit the data. Then, the EPA only audits a very small portion of the cars of any given model year by conducting its own tests.
In general, the EPA has been criticized overall for this approach and for having a testing procedure that doesn't accurately reflect the typical American's driving habits. In addition, many feel the procedure does not effectively account for hybrid powertrains, which were not around when the test was first developed decades ago.
The good news is that the EPA is considering changing its testing procedures for calculating a car's fuel economy, especially for hybrid cars. If that occurs, the fuel economy numbers you see on a car window sticker should more accurately reflect what you can expect driving the car.
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