There seems to be a bug with monsters attacking up staircases. Specifically, I'm getting attacked by monsters on a different vertical level while standing exactly two spaces away from the stairs (rather than on top of them, the way it's supposed to work.) I'm not sure if it's a general "monsters-can-attack-through-floors" bug or what. I haven't seen this bug before, so I'm not sure when it appeared.
EDIT: Also, I really, really suggest fixing the "looking at yourself or an ally makes you hostile to your own faction" bug before the Steam release. I don't know the underlying code, so I can't say for sure, but I assume it wouldn't be too difficult, and that bug is unbelievably nasty for certain builds (especially if you combine Temporal Fugue with other allies of any sort, or if you use Burgeoning at all.) It tends to happen eventually, since all it takes is one careless 'enter' while looking to irrevocably leave you hostile to yourself.
If the bug can't be fixed in any other way, perhaps a config option to remove the ability to target stuff via 'look'? There's already a "select target" option, and while presumably you can still cause the bug by hitting yourself with that, you're less likely to do so by accident (since I think the problem is caused when I use 'look' to check the health of an ally, then make the mistake of hitting 'enter' -- I don't want to be able to accidentally target allies while looking at them if it's going to cause this bug!)
Also, while mostly-unrelated, if you have both Beguiling and Proselytize, an older ally recruited using one will continue to attack a newly-recruited ally using the other. This wears off if you leave the area, unlike the 'hostile to own faction' bug, and happens even if you aren't yet hostile to your own faction.
(Oddly, it seems that hostility to your own faction doesn't cause Beguiling / Proselytize allies to attack each other, though it does make Burgeoning plants attack each other and makes Temporal Fugue copies attack any other allies you have.)