One problem related to transmission noise has been reported for the 2006 Ford Fusion. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Ford Fusion based on all problems reported for the 2006 Fusion.
Purchased 2006 Ford Fusion sel 6 cyl. , with roughly 48k on it and currently have 62k on it now, in/around October of 2009, and about 3 months ago starting having transmission problems. Upon accelerating between 25-40, the transmission jumps in and out of gear, often making a loud banging noise and taking away all acceleration. In order for it to get back into gear, you have to completely let of the gas and it will eventually go back into gear. This allows for minimal accelerator at best when trying to speed up. This failure occurs randomly everytime I drive the vehicle. If not fixed, the transmission in my car will eventually go bad. I took it in to advanced automotive in ann arbor to have it fixed. They told me, after doing extensive research due to no codes showing up on the computer, that on the Ford bulletin it was going to need a new valve body, transmission flush, and reprogramming. This is going to cost roughly $2200. The valve body, from Ford, was $1400.