Dental Issues with 3 year old

My three year old son had his first real dentist visit last year at which point the dentist gave him a fluoride treatment as he said that his teeth were easily pitted. By the time we went to our next visit he had developed strange brown spots mostly on his canines and the surrounding upper teeth. These spots would not rub off and were like a film. Our dentist had no idea what they were and jokingly asked us if he drank a lot of coffee and smoked cigarettes! I have since come to the conclusion that this is a result of too much flouride in his system. I have reverted to using a non-flouride toothpaste. The stains are still there, we scrape them off every once in a while but they return, just less so than before. Is there a homepathic solution out there that would help with strengthening of my child's teeth? I would appreciate some pointers.