Is that because the allies keep getting "confused" or made "friendly" by the enemy via "mass confusion" or "big hug"? In version 0.2.7, I addressed this by lowering the incidence of "Big Hug", "Confusion", and the dreaded "Mass Confusion". I also added state resistances to the weapon fragments and resistance stones that should help the allies better fend off these spells. If your issue is not caused by enemy spells or has not been made better by these adjustments, let me know and I will dig into it further.
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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.