This might help, if I understand you correctly that is. If you click on your soldiers buttons ( where you assign stuff such as reaction time shots ), on the far left one, if you click on it the choice of which attack you want to use ( Aimed shot, 5 round-burst, etc ) will become available. Click on which attack you want to use, then try and see if you can target an alien. If your just mousing over the alien before doing this ( red box around it ), you cannot target him. If I've misunderstood your question, I'm sorry, but this is about the only thing I can figure out that is happening with your issue. Maybe one of the Dev's can give you more input if this doesn't help you.