It does NOT appear that they are friendly or confused, which is why I am so frustrated. It's super weird.
I think this is a targeting usability issue and I have seen it sometimes. If I have my mouse hovering over an enemy but I am trying to target with the arrow keys, I sometimes have to move the mouse and click over the enemy. What platform are you using? Mac or PC? Anyway, there is no reason for a player to target allies in a physical attack so I took that ability out so that should relieve a lot of the frustration (that fix will be in 0.2.8 when it eventually comes out). I kept the ally targeting ability in for many spells so that they can be reflected to the enemy, but if the targeting is still providing usability issues, I will take that out too.