City pathfinding is bugged. If there is not enough space in the city for the moving army it will not pass through the city. instead it will plot a path around it.

 This is one of the most annoying things ever. In order to fix the problem I have to make the army in the city or cities along the path move elsewhere leaving them undefended.

 It also causes units to take a route that can literally circle most the continent in order to find a path that is not blocked by a city. So instead of a path that should take 5-6 turns it turns into a path that takes 20-30 tuns. Not to mention the loss of a couple turns movement if you do not want to take the route. Soon as you click the unit moves along the crappy route wasting your moves for that turn and the following turn to get back to the starting position.

This also chokes AI units as they can not pass through their own cities or other player cities. 

I used raise land to create a pathway for my units to bypass my own city only to have it clogged with AI units within a few turns rendering the new path useless.

To me this falls into the major flaw category.