The AC evaporator drain hose may become dislodged and cause a water leak on the passenger floor.
Car problem reports
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Newest reported 2006 Scion xA problems
An illuminated Check Engine Light could be caused by a defective VVT-i controller, which changes cam timing for optimal power. Updated parts are available and the repair may be covered under the powertrain warranty.
Air conditioning that doesn't blow cold enough could indicate the need for adjusting the cable for the temperature blend door.