1. Had to replace the alternator at 20,000 miles after the car died on me a few times. Covered by the warranty
2. The car gets very very easily dented. To prove it both side doors have dents made from other car doors.
3. Paint tends to chip very easily. I have to apply touch up paint very regularly.
Overall comfortable car to drive although the interior is a little noisy at highway speeds.
Major gripes:
1. Easily dented (should be called Civic "soda can")
2. Brakes wear out frequently.
I don't understand Civic brake complaints. I just replaced the front pads on my 98 Civic EX 5-speed AFTER 104,000 miles. They still had 1/8" of pad left on them. I have never had pads last more than 50K on any other vehicle.