More than likely it is intended. You have to think about it when a inland town is set up next to a river it is more than likely using that river as a source of water. If the river runs through the city it has a chance that it will become polluted or if you have a wall around your city it means that there are large gaps in your wall that could be exploited during an attack. A coast city on the other hand while it does have those same problems they also have the benefits of boats coming to and from so having the city set up with the river running though it would help with trade.