I just had my first base defense mission, and it was messed up in several ways that screenshots don't quite capture. I forgot to take screenshots during the mission, and when I reloaded the autosave the game didn't load the same way (issue #1 no longer applies when I reloaded the savegame).
1) All the invaders were in various parts of one room. Two of them (Sebalian and a drone) were apparently in some "entryway" beyond the walls of the room. There was an opening, but I couldn't go into it (or even within 2 tiles of it). I couldn't shoot into that room through the doorway (although I could shoot through a wall and hit the Sebalian). I could throw grenades into the area.
2) I stunned an alien, and after I moved I noticed there was another stunned (blue) alien about 8 tiles away, no way I could've accidentally stunned that one. Later, I stunned another alien maybe 20 tiles away, and the magically-stunned alien "woke up".
3) I had a severely woulded soldier who would bleed out the next turn, so I stunned them to save their life. It worked, in that my soldier didn't die (wounded: 17 days), although the end-of-mission report gave me -1 for loss of one Xenonaut. But now this soldier is in the hospital for 17 days, but still assigned to Charlie 1. Since they're wounded I can't un-assign them, and since they're wounded they can't go on missions, so I'm down one soldier for ground combat until they're at least 50% recovered.
edit: adding screenshot. It also seems silly to have all the aliens invade in a huge clump like that. If they always do that, a couple rocket launchers would solve the base defense mission in one or two turns...