The automaker says it is aware of the problems, and is working on solutions. Auto tracking firm J.D. Power revealed similar criticism this summer, so the automaker was already aware that consumers have been complaining about some products.
"Our internal surveys now show that we are largely back on track after addressing these near-term quality issues," the automaker said in a statement.
The Dearborn, Mich., automaker had made strides in quality improvements in the past few years, narrowing the quality gap with Japanese brands. But Toyota, Honda and Mazda held on to the survey's top rankings, making up nine of the top spots this year. Chrysler's Jeep brand was the best-ranked U.S. brand.
Although the rankings are influential and important, criticisms from consumers today sound nitpicky compared to what quality rankings used to find out back in the 1970s and 1980s. Back then, consumers routinely complained of parts falling off cars or other major problems that resulted in vehicles heading back to the dealer for days.
In comparison, the complaints about Ford seem inconsequential. But Dave Champion, senior director of auto testing for Consumer Reports, said it's important for consumers, who are spending extra money on these technologies only to have them freeze up. Or even worse, force car owners to head back to the dealership to have the system updated.
"When you are looking to buy a car, why should you have to put up with something like that?" said Champion at the Automotive Press Association luncheon, where the survey was released.
The problematic touch screens are called MyFordTouch and MyLincolnTouch, and can be found on the Ford Explorer, Edge, Focus and on the Lincoln MKX. The transmission problems were found on the Fiesta and Focus, in the new PowerShift dual-clutch automatic gearbox. That transmission was jerky at low speeds, and often felt like there were problems at highway speeds as well, Champion said.
The full report can be found here.
For the fourth year in a row, Toyota's Scion, a brand geared toward young people, had the fewest problems, followed by Toyota's Lexus brand, Honda's Acura, Mazda, and the Honda brand overall. Lexus, a perennial top finisher, recovered from a fall last year, rising seven spots on the list.
Scion was tops because the two models covered in the survey, the xB and xD, have been built for several years and the bugs have been worked out, Champion said. Champion also said Mazda improved because its current models have been out for several years.
For the most part, older models have better reliability than new or revamped models, said Champion.
At Chrysler, however, new or significantly revamped models led its resurgence. Champion said the Chrysler 200 midsize sedan, and the new Jeep Grand Cherokee and Dodge Durango SUVs helped the company improve its ranking.
"They seem to be totally transfixed on getting it right," Champion said of Chrysler. "It was in many ways 'Do or Die' for Chrysler."
Chrysler has been plagued by reliability problems for years but has been improving since the U.S. government put Italy's Fiat in charge after Chrysler's 2009 bankruptcy filing. The Chrysler brand moved up in Consumer Reports' ranking from 27th last year to 15th this year. Jeep rose 7 spots to finish 13th.
The Associated Press contributed to this report.