When Rorschach goes to talk to Manhattan for the first time, due to the extension of the dialogue with the "possibly homosexual" line, Rorschach delivers his line late to Manhattan. However, they didn't change the shot, and if you look closely, you can still see Rorschach's mask moving slightly, saying the line at the same time he did in the Theatrical Cut, but of course the line is not there, so, he's just moving his mouth.
It kinda annoyed me.
Says what line? If you mean him saying "Doctor Manhattan," he says it at the exact same time he does in the TC. It was unchanged.