I have noticed that the aliens get clipped into the walls in the base at times? Also I just had one game were the soldier was moving through an upstairs room fell through a hole and kept running when he hit the wall on the lower level he kepts running on the spot I could not stop it I had to quite the game to stop it and now it will not load at all? I will try a restart on the Mac if does not solve it I will just start again. So far I have not been able to complete a base defense as when the base is cleared it just says alien activity and I can never find the last (if any aliens) so cant end the game, this has been three times now? There needs to be some kind of marker to show the location of the last aliens so you can hunt them down, but I think they are clipped into the walls, so this is why a marker is very important.
just like in this thread: 
and
They are in the walls. Just search for a light cone on the wall. You have an example in this video from 37:32
Xander made few mistakes here, but well, it was one of his first missions to defend the base. Just remember to take Hel Cannon on such mission. - If you will find such light spot then aim and fire in that place. projectile will go through the wall. One shot - one kill.
When you do find them you can’t kill them the wall stops you! BUT… They can kill you! I had one run out of the wall shoot me then run back in the wall and I just could not shoot it even at point blank! But I am still enjoying this game can’t wait for it to be ready!
Like i said. Use Hel II Cannon (heavy cannon) - the one which makes 18 damage. One of your heavy guys should have it as standard equipment. It can pierce walls.
Thank you! I will try it…