I get this all the time (especially during first base mission) that the "can see enemy" icon at the right appears, but the light drone it refers to is invisible, and cannot be attacked. So I have to wait for it to move or attack me.
Note that this doesn't refer to me not having line of sight, as far as I can see. Normally, you can see the model of the enemy, greyed out, if that occurs. The light drone is simply not there, and clicking the right hand icon centres the image on where the enemy is supposed to be, but still nothing.
I tried to use the multi-level option to see if the drone was higher up, but nothing either...