Continuity mistake: Godzilla noticeably changes size throughout the movie. For example, he is shown lairing in a subway tunnel, but he cannot fit into the Hyde Park tunnel (taxicab scene), which is significantly larger than a subway tunnel. Also, compare the size of Godzilla's eye next to Matthew Broderick during the fish scene and Godzilla's death scene. The eye is way bigger in the latter.
Continuity mistake: When the Mayor of New York is talking to the crowds and people can feel the ground bouncing, Godzilla is a fair bit away, but when he is stomping through the streets the people don't feel it at all - shouldn't they be thrown into the air from that proximity?
Continuity mistake: Near the end of the movie there are 3 US Navy F-18 planes. The lead plane shows a graphic of 4 missiles, 2 of which he launches at Madison Square Garden. Then later, and without landing, the 3 planes fire at Godzilla, 2 missiles from each plane on both passes. This means the lead plane fired 6 of its 4 missiles.
Continuity mistake: The first footprint - the one Nick is standing in - is clearly smaller that those shown from the helicopter (watch the toes).
Other mistake: At the taxi cab chase at the end, you can notice when the car is a real one and when it's CGI. Note how the real car has scratches and other things on the front of it, but the CGI car, if you look closely, has almost no imperfections, and even if it does have some, it doesn't match the real car one bit. You can see these things when the car drives off his mouth or when you see Godzilla running behind.
Continuity mistake: When Godzilla is chasing the taxi, the taxi crashes through a chainlink fence. As it rounds the corner shortly after going through the fence, the sign on top of the cab comes loose and is being held loosely by a wire toward the front of the cab. You can clearly see that the sign is loose, but a few shots later, the sign is attached firmly in place atop the cab.
Continuity mistake: As Godzilla is about to step on Animal, we see two cars are directly behind Animal (a yellow taxi and a gray car). Each shot of Animal from the front as the monster approaches (and he's trying to get the tape locked into the camera) shows portions of the cars. But in the side shot of the foot as it lands, no cars are right behind Animal at all.
Revealing mistake: When they are climbing up from the subway tunnel into Madison Square Garden, there are lots of half-dead fish scattered around from when Godzilla was feeding. Right before they enter the arena, in the overhead shot looking down on the actors, there is a wiggling fish in the lower left portion of the screen. If you look closely, you can see a string attached to the fish. A crew member is obviously tugging on it from below, to make the fish move.
Continuity mistake: When they are tracking the monsters movement towards the pile of fish, on a computer screen the icon representing Godzilla moves forward and in the next scene repeats over the same territory.
Factual error: The Apaches in the film are depicted with dual machine guns on each side of the cockpit, mounted directly on the windows. In real life, Apaches cannot mount such cannons, and instead use an M230 Chaingun in a turret underneath the helicopter, which the film Apaches have, but for some reason do not use.
Continuity mistake: During the scene right after the F-18's destroy Madison Square Garden, Godzilla goes after the taxi and Nick tells Phillipe to turn the car around. The problem is that on the street you can see that the first time they went through, Godzilla left some huge footprints and destroyed the street. When they turn around and drive up there a second time, the street is perfect. This happens again when they are stuck in the Hyde Park Tunnel and Godzilla shoves a claw into it and breaks up the road right in front of the taxi, but when Phillipe drives forward and then puts on the highbeams, the road is fine.
Revealing mistake: When the two soldiers are in the subway tunnel just before Godzilla's eye opens at the end of the tunnel, check out the beams on the flashlights. When the flashlights shine on the walls of the tunnel, they are normal. When they shine FURTHER AWAY onto Godzilla, the light beams get narrower and more laser-like. The circle the light makes on a surface loses the dark circle in the centre when it shines on Godzilla too.
Revealing mistake: When the old guy is running down the pier as Godzilla smashes through it it's very obvious that he was just cut in from a bluescreen. The water never touches him even though it gets passed him and he runs straight even though the pier shakes and bends right under his feet.
Other mistake: It's difficult to spot (it's easier on DVD, but I don't have the timecode). Godzilla has just left Central Park after suspecting the trap with the fish. As he rumbles down the street, hundreds of Apache helicopters swarm in and attack. When they begin firing their cannons at Godzilla, if you look carefully, you'll see the tracer fire from one gunship overlap over another gunship. The cannon fire is heading away from the camera and getting smaller, so it should at least go through the other helicopter and disappear on the other side, but it remains superimposed on the Apache. A little special effects mistake.
Continuity mistake: In the scene when Victor is chasing Nick after crossing the airport sign on the road, you can see the steering wheel of the van is being held in Victor's right hand from his point of view inside the news van, but in the next shot Victor is holding the steering wheel with his left hand.
Continuity mistake: In the scene where Mathew Broderick is loading his luggage into the taxi, Hank Azaria is seen opening and holding an umbrella. When he crosses the street to steal a truck, he drops the umbrella, but on the wide shot that soon follows, there is no umbrella on the ground.