Running 2.2.1 so it might have already been fixed, in a mission, the one with the cliff and 2 houses if that helps, there is a large rock near the top of the cliff that an alien will, more often than not, get stuck in. I then can't kill this alien, it's possible to get your own men inside too but they can be moved back out. The only way I've found to complete that mission is to abort it and lose the entire squad. When I get hold of the latest stable release I'll see if I can replicate it again.
Running under Open SuSE 11.2 with the build in the pacman repository for that version
