Searching showed a lot of people with the same problems as me with custom siege maps and their pathing. Then I saw a bunch of the bugs were just dismissed because of a lack of screen shots. I've attempted to add some screen shots, technically they are pics I took on my phone because my screenshot command won't work for some reason in game.
In these screen shots I am defending on Basel castle siege. The problem is the defenders all want to group up inside the castle wall and keep running into the wall trying to run straight at the enemy. They mostly ignore any commands that PC gives to try to move them to a logical place. And then the attackers all try to run across to the same point and they end up just running into the wall on the other side of the defenders. There are a few that trickle across the draw bridge slowly and then like 2 defenders will turn to attack them when they get close. For reference I've played this same siege map as an attacker and had the same problem.
http://d.pr/i/QzOe here you can see the defenders running into the wall like idiots, the gate is way off to the right.
http://d.pr/i/dkx3 here you can see the attackers are standing on the edge of the moat while 2 guys trickle over the drawbridge randomly