This is just some general information about some of the issues I have been having with flanking and my general observations. If any other player has any info to add to this, please do. I have been working with the devs to figure out what this bug is and how it happens.
It appears that your unit can get flanked if you are using one (or more) of the terrain features to hide behind or to protect your flank. My first bug happened this way, almost like the bad guys ghosted around it to hit my side. The other way this seems to happen is if you overlap 2 or more of your units with the idea to keep a solid front toward the enemy. Bad guys seem to be able to exploit this overlap and flank somehow.
I am still trying to get more info in order to nail down what is happening and how, but if anyone else has any insight on this. Or if it happens to you, try to post here what happened and as much as you can remember, so we can stomp this bug.