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.
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 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)