Well the   hidden enemies can  be fixed by making the  sides of doors and big  rocks  in  planetside  work as cover. Also the enemies  clip through the walls  so they can shoot through thing you cannot which is a issue. As for your main issue i have had that  too i am going through a door an my shots  go way up above me like they are shooting the frame of the door and nowhere near where they should be  hitting.    

I've had these issues as well. Also have a strange issue on interior missions where one of the little nurglings will run at me and start swinging it's little arm blade, but never connecting and I can target it, but I can't hit and kill it and it just stands there swinging it's blade, but doesn't chase me. 

It seems that game prefers to target what is on top of your cursor. And due to bad camera view, you often target walls and columns instead of enemies or ground behind those objects. I think game should clip a far larger part of obscuring terrain, not in your closest vicinity. Without that you can't shoot at long range most of time as enemies are either hidden by terrain or outright untargetable.