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.
Car problem reports
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Most reported 2006 Scion xA problems
The AC evaporator drain hose may become dislodged and cause a water leak on the passenger floor.
Air conditioning that doesn't blow cold enough could indicate the need for adjusting the cable for the temperature blend door.