Ever since the aliens started always leaving a couple of guards inside their UFO's, I've noticed this very aggravating issue. Basically, it's almost impossible to actually hit aliens inside UFO's. I've mostly tried light scouts, since it's hard to go far into the game with this issue.
What happens is this: I reach the crashed UFO and park six soldiers in a 2x3 formation right outside the door, two heavies in front and the rest riflemen. End turn.
I open the door and spot one or two aliens. Since it's a small UFO, the distance is about 5 tiles. I target it with a heavy and the accuracy indicator usually says something around 10-20% chance to hit. I fire - every shot misses. I pick the next heavy. Every shot misses. Repeat for all four riflemen - if I get lucky, I hit with one or two bullets. I move them all out of sight to prevent counterfire. End turn.
I move all soldiers back into the 2x3 position in front of the closed door. End turn.
Repeat for maybe six to ten turns until I've hit with enough stray shots to actually kill two caesans. During that time, I've probably fired a hundred bullets or so.
I've even tried running up and standing right next to the targets, firing full auto with both riflemen and heavies. The accuracy indicator at that point usually says 50% or so, but still I usually miss with all bullets. The bullets will literally go straight down into the floor or at a 45 degree angle to avoid the alien.
This happens every single ground mission.