On the traintrack map, I had a soldier behind a single level crate crouched down and went to shoot an alien and it shot the crate in front of him.
I have to stand up and then move 2 tiles to the left or right to get a line of fire, from behind a single crate. Then I have to run back behind and crouch again to avoid getting hit myself.
I also posted this in the guruofreason post in Suggestions & Features and told to repost it here as maybe a bug.
http://www.goldhawkinteractive.com/forums/showthread.php/4540-Cover-blocks-the-person-in-cover-s-fire-%28fix%29