Occassionally this happens and the best course is to remove the suture. In my experience, most often this will not affect the result as there is good scar tissue supporting the "new" shape by now. If there IS some "rebound" toward the old shape, you may resuture that spot.
A permanent stitch that has perforated the skin must be removed because it will otherwise become an entry point for bacteria which can then lead to an infection of your ear.
The permanent sutures used in the Otoplasty procedure can occasionally push through the skin. Often they can be removed safely in the office without difficulty, but may need to be replaced if the result is affected adversely.
See your surgeon to evaluate your options.