Just wanted to show how bad it can be marked with the red squares.
In this screenshot I decided to build a road network just so my allies could go to the SK and get sacrificed instead of standing idle, blocking MY roads. F
From this screenshot you can also my army wanting to move past the wraiths (illustrated with the green dots), but because the wraiths are very aggressive my puny hero Varda does not dare go near these spooky things. Therefore I have to manually move around them. Further the path finding algorithm does not know the fear of my units and hence just calculate an optimal route without regard for my units well-being, sigh. At least if the path finding algorithm could take into account that the allied units wont share a tile with me, and therefore make a route around them, it would not be such a big problem. Right now you must micromanage you unit, if you want your unit to move a long distance due to the unit getting stuck behind one of the allied units.
https://flic.kr/p/rr1AvE
Updated: Screenshot should be working again. Have used Flickr now.