Plot hole: Change in hotel clerk
Let me start out by saying that I very much enjoy this movie. Perhaps it helps that (back in my movie-going days) I was a big Tarkovsky / Grennaway / Kurasawa fan. In other words, I like visually stunning films, and this one measures up.
But yes, there are plot holes: things that make about as much sense as (pick any Tarkovsky film). Personally, I just ignored them. I was so caught up in the visual opulence of this piece that I didn't let the oversights and inconsistencies bother me.
Nonetheless, I figured I'd point out one that I haven't seen mentioned up until now.
When Murdoch comes downstairs at the start of the movie, the guy at the desk is a balding white guy with a moustache (who reappears in another job later in the movie). When Inspector Bumstead arrives to investigate the murder, the guy at the desk is a large black guy. I understand why the film does this: to puzzle us... to make us wonder why there is a different guy there than before, who claims to have talked to Murdoch, which we know isn't true. Its function is to disorient us, and make us wonder what is going on. Fair enough.
Only one problem: it's still the same "day". There has been no intervening "Tuning" (otherwise John Murdoch would have noticed it), and the Strangers do not (anywhere else in the film) swap people out between "Tunings". How would they? Wouldn't everyone notice? "Hey... don't mind us... we're just going to drag this little guy out of here and put this big guy in his place... you can all just pretend that he was always there." Doesn't really work.
As I said, it didn't spoil the film for me. I understand why that detail is there from the point of view of storytelling. I just thought I'd comment on it.
I think that it's things like this that irritate some sci/fi lovers. Unlike The Matrix, which tried hard to create a completely consistent world (which is pretty easy if everything is inside a machine... free license and all), Dark City tries to create a consistent atmosphere, and sometimes in doing so plays fast and loose with "factual" details. Didn't bother me, because I'm in love with the visual aspect of the film, but I can see how it would irritate others.