As a simple example, United probably isn't going to offer a flight where one leg is on United and another is on American. Yet, it might be substantially cheaper or less painful to take that flight. Certain codeshares may be more profitable for them to hawk, to the point where they will only show certain legs when the more profitable flight is booked. They may also choose not to show flights that are already profitable based on bookings (e.g. takes 75 economy seats to make flight with legs A->B and B->C profitable) when a similar flight (A->D, D->C) is underbooked and could use some more folks aboard. There are probably a thousand other reasons...