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.
2004 Scion xA Problem Reports
Most Reported 2004 Scion xA Problem Reports
When backing up and applying the brakes, you may hear a squeaking noise. Scion engineers addressed this problem by modifying the shape of the brake pad and the anti-squeal shims; they also applied more grease during assembly.
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.