One problem related to transmission slip out of gear has been reported for the 2004 Toyota Matrix. The most recently reported issues are listed below.
2004 manual Toyota Matrix xr 1. I was hearing a very slight tinkling sound when at low rpms in 2nd, 3rd and 5th gears. When the clutch was pressed the sound went away. The sound was occurring for about 2 weeks before the failure. 2. Complete failure of the transmission. Driving in 5th gear and there was a whirring sound, a clunk, and the car jumped out of gear. Could not get into 1st, 2nd, 5th, or reverse. When car is neutral it is still in gear. We had significant trouble towing the car as I had to be inside the car with the clutch down as the tow truck driver pushed it. 3. Replacement of transmission.