I didn't have a problem either except for one scene: his takeover of the stock exchange. That's was it. However, there is an obvious break in the effect during the first fight scene - Hardy's natural voice came through loud and clear.
I, too, also noticed that Gotham was obviously Manhattan Island this time. At least in the first film, there was some attempt to hide it. My inner geek was a little peeved at DC for having fictionalized the names of cities in the DCU in a manner Marvel never has.
I don't think this was the best Nolan Batman film if you're judging location shooting continuity. It was too sloppy with the Freedom tower and obvious New York skylines.
At least for "Batman Begins" and "The Dark Knight" you knew Chicago was the primary location and not 3 different spots
Still, if you don't pay much attention it blends seamlessly.
LA to Pittsburgh to New York and back to Pittsburgh.
There was a lack of consistency. In Batman Begins we get a very stylized fictional Gotham. In The Dark Knight the stylized city is gone and it could be any major city. Finally we get a dead ringer for Manhattan although some of the filming was in Chicago.
They never went back to Chicago for the third film
-Bruce returns and Selina saves a boy
-Batman returns after 8 years and follows a police chase
-Gordon meeting the cop at his house
-Heinz field for the football stadium
-Bruce leaving Wayne Enterprises after he's left as a board member.