Another plot hole was that Dan tells Laurie that the Manhattan cancer connection makes no sense because SHE doesn't have cancer, but how would he know that for sure just by looking at her? In the comic she's screened when they kick her out of the complex, but that's not shown in the movie. This probably won't be a problem in the extended cut, though.
Other stuff that may be fixed in the extended cut are the Rorschach flashback scene I bitched about earlier, the man on the street perspective (which makes a world of difference to the ending), and MAYBE some of Ozy's characterization (though there's only so much you can do with a performance like that).
But one thing that'll always make me cringe is the part where Dan and Laurie cross Walter Kovacks in the street and there's a shot of him, and then a shot of Dan looking back. Why couldn't it be a long shot with the guy just standing there, waiting for the watcher to notice on second viewing? Why does every clever detail have to be a close up? That's indicative of everything I hate about Snyder's directing (AND THE WORLD), both in style and in substance.
