Let consider context (e.g. historical recent past) where modern meaning of missile as a self-propelled ordinance with reactive or jet engine doesn't exist.
Then its original meaning is "an object which is forcibly propelled at a target, either by hand or from a mechanical weapon" (Oxford). How it is different historically it was from projectile (if it was), which same source defines as "a missile designed to be fired from a gun" or "an object propelled through the air, especially one thrown as a weapon".
Were they full synonyms, were they used interchangeably or projectile had appeared later?