We know that between the 23rd-28th day of pregnancy the trachea and esophagus divide into two tubes. What can cause, if anyone knows a cause, something to go wrong with the division?
No one really knows, but the blood supply changes abruptly in mid-esophagus. We know that in other areas of the intestine, cutting off the blood supply will result in atresia. Why this happens in an individual during pregnancy is not known. We know of no association with any pregnancy events, drug taking, etc.