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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.