Sometimes I've been able to spot aliens directly through building or UFO's walls, even from the outside of UFOs.
So I will try to explain clearly what is going on here:
- This game is deeply broken.
- Many game mechanics/features are hidden from the player, and you can't realize how broken the game avtually is. You must dig in the xml files and the game code to see that.
- Solver is doing a great job fixing a lot of thins in the X:CE mod, but sadly it's not enough, too much of a job for a single individual. New bugs and broken mechanics are still being discovered.
- The very same developers have stated the game engine is NOT APPROPRIATE for this game, but they realized too late and a lot work was already done.
Don't take it too harsh and just try to enjoy th game as it is, install some mods, the X:CE, etc... The game will still be broken but you can have some fun, if some situation is just plain wrong, like the one you described just reload the game. Or else quit gaming and play/wait for other games.
Cheers!!