When Shredder assaults the Turtles hideout where Raphael is leaning over Splinter, the scar on Raphael's lip changes from left to right, as does the hole in his sunglasses changes from right to left lens, indicating that this shot was reversed.
At the end of the movie during the beginning of the fight scene atop the Sachs tower you can clearly see that One World Trade Center is just a few blocks away but then during the remaining of the fight we see that the Sachs Tower is back in midtown and One World Trade can be seen way in the distance.
Scott Mednick, the executive producer, stated that this film will be live-action. Link. The Ninja Turtles themselves however will be computer animated through Motion Capture, as opposed to using practical effects.Link.