One problem related to manifold/header/muffler/tail pipe has been reported for the 2006 Toyota Matrix. The most recently reported issues are listed below.
46,686 miles and the intake manifold gasket needed to be replaces as it was a defective gasket- hard with bubbles- I have the gasket. When I called Toyota I was informed that it was an issue with this make/model, but Toyota wouldn't reimburse costs of replacing the defective part.