One problem related to transmission noise has been reported for the 2006 Audi A3. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Audi A3 based on all problems reported for the 2006 A3.
My wife is traveling a long trip. She is driving a 2006 Audi A3. She had been having weird things happen during her trip. It started when she made a right hand turn from a stop sign. She pushed the gas, but the car did not move for a few seconds and then it went. This happened a few times, all the same sort of way. Then after a right-hand corner turn, the car made this huge noise and clunk upon acceleration. Again, it drove ok after that. However, the big unsafe problem first occurred @ apx. 49,870 on odometer, ironically, just before the warranty was out. She was driving about 45 mph & backed off of the gas to slide in between two cars & then pressed on the gas to accelerate to the speed of the moving traffic & suddenly without warning, the car seemed to go into neutral but because the gas was increasing, the engine kept revving. She seemed to coast, no increase in speed. The car behind her swerved over in time, but it was too close! she backed off of the gas or braked, she couldn't remember and the car clunked into gear. When she called me, the car had 50,150 & she was concerned because this had just happened a 2nd time. It happened the same way, when she was accelerating. I called my local Audi dealer & spoke with the service manager who agreed to provide a free diagnostic test. We have since discovered that there is a recall for this same problem in effect for the 2007-2009 Audi (including A3) as well as for 2007-2009 vw's with the same transmission problem. 2006's need to be included in the recall too.