Hi
I have had this happen too, and most of the time if they are born right on, they come back to it. I have also had babies who appeared off when born, when there teeth come in (first ones in a couple of weeks) they are right on.
In any case I have all my babies checked by a equine practioner prior to them being 6 months old. Most of the time (except in rare occasions), this can be corrected with a simple float usually on the front teeth. Many times the teeth are simply to large/tall for the mouth and get caught on each other as their mouths grow - and when this happens it prevents the jaws from growing correctly. Sometimes only floating will help and must be corrected as soon as possible - preferably during the first six months, since the babies grow the fastest during that period of time.
The equine dentist/practioner should be able to tell if it is something that needs correction, or will correct itself.
Good luck,