Museum – While perhaps this isn't even a problem, it seems rather odd to me. Certainly, the Security Guards are, in a sense, innocent(save for the fact that they will try and kill you on sight), but to lose humanity for killing any of them, pretty much forces one to sneak through the place without killing a single guard. This can certainly work, but the problem it brings about if one already has a low humanity(Say 3 or 4), before this part. If so, then it means that killing a few of the guards in the main area of the Museum or any of them in the basement, will result in a game over,.
This might be intentional, but given that there may be little way for one to raise it, or if the sneaking route is not really an option, then it might not exactly work.
Otherwise, I thought there was a problem in the Internet Cafe, as the usual pc used for the main quest did nothing. Though it was because of a reload in the cafe(fixing a texture I edited), but obviously it isn't an issue, since it's another pc that needs to be used.
Thought I saw a spelling error somewhere too, although I forget exactly with what. It might've been one of the items, maybe the book needed for Akeem's quest, or the Baali book. I'll have to check, if it is something I can still take a look at in my game, or in the files.
Also, the “blood” spatter in the stealth kills(at least for the Fire-ax, have not seen the others yet), are white. Likely due to the Shade, and not specifically a problem. I have not had any success editing the particle images anyway, so I don't know if new ones will take.