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.
Gotham City was modified version of Chicago in the first movie (tit was filmed here). Wayne Tower was a Modified version of our Board of Trade.
In The Dark Knight they decided to jettison all of the CGI modifications and used a largely untouched Chicago (With some scenes being filmed in Hong Kong).
This movie was clearly New York which was a bit jarring. Most of the time its not that big of a deal, but there are scenes where you can CLEARLY see them building the New World Trade Center, which given the theme of the movie is hard to ignore.