One problem related to transmission failure has been reported for the 2006 Toyota Matrix. The most recently reported issues are listed below.
I was returning home last week on I-40 in TN. I was going up a grade with vehicles all around me when my transmission blew. I instantly lost power and went from 70 to 50 in the blink of an eye. Luckily I wasn't hit and was able to get the car off the road. After towing the car home I was disappointed to hear of many similar accounts from other Matrix owners. Apparently there are faulty bearings to blame for countless transmission failures on cars with alarmingly low mileage. This is something that Toyota should reconcile with its customers and more importantly, fix before someone is injured or killed.