Continuity mistake: The first footprint - the one Nick is standing in - is clearly smaller that those shown from the helicopter (watch the toes). (00:11:05 - 00:12:25)
Continuity mistake: Nick and company are in a plane after leaving Tahiti. A soldier goes up to the colonel and tells him about the fishing trawlers that were pulled under. Just after that, the camera shows three guys sitting down that look up. In the following shots those guys are gone. (00:19:50)
Revealing mistake: When Godzilla attacks the fish market, the creature picks up the seafood/fish truck with the driver still inside. As he's being knocked out of the cab, you can see dozens of boxes set up where the truck was once parked for him to land on. (00:26:00)
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. (00:29:50)
Factual error: When Godzilla first attacks New York and then disappears, we are shown the MetLife Building, which has a massive gaping hole in it. The immense structural stress of a gigantic lizard smashing through the building, not to mention most of the center supports being taken with it, should have collapsed the building, yet it still is standing. (00:33:35)
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. (00:49:25)
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. (01:09:40)
Other mistake: When they are tracking Godzilla to the second pile of fish in Central Park, the tracking device says that Godzilla is moving with a speed of 175 mph. If you look at the shots before it with the soldier looking over the top of the building, it is impossible for her to walk at that speed. (01:18:15)
Continuity mistake: Godzilla noticeably changes size throughout the movie. For example, she is shown lairing in a subway tunnel, but she 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: 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.
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: 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.