Sometimes aliens cannot be targeted just by hovering mouse over them.
Like on this screenshot (gray circle under the alien is the mouse pointer):
http://steamcommunity.com/sharedfiles/filedetails/?id=209483743
Had the same issue in V19 stable.
I've tried to restart the game but it appears to be a stable bug.
Not so much of a problem as the shooting can be enforced by CTRL or just clicking on the weapon icon first, but this is obviously not how it was supposed to be...
Here is the game save file to reproduce this behavior