Revealing mistake: When Johnny and Reed are talking about the bachelor party in the lab, they keep moving from one side of the table to the other: One side has a green book, the other a red one. Note the books behind Johnny and you'll notice by the colour and the reversed text that the shot's been flipped.
Revealing mistake: At the end, there is a group of people with their backs to the camera, facing & waving to the Fantastic 4. As the F4 fly towards the camera and out of the shot, the crowd turns to continue waving to them. One small boy in white remains facing the wrong way, still waving, until another child grabs the back of his clothes & turns him to face the right way.
Continuity mistake: As the Silver Surfer and the Human Torch fly down the face of the sloping Grace building, traffic on 42nd Street, below, can be seen moving to the right. When they hit the street level, traffic direction has reversed relative to the building. The number of lanes visibly reduces from 6 in the above view (2 parking lanes, 2 traffic lanes in each direction separated by a double yellow line) to 4 at the street-level view. This would also qualify under another category, as 42nd Street traffic is two-directional. The first, high angle shot from above correctly depicts the actual conditions on the street.
Factual error: The Human Torch chases the Silver Surfer into the Lincoln Tunnel at 29:35; the entrance shown is on the New Jersey side of the Hudson River (although they had just been in Manhattan seconds before, they were airborne and could have gotten there from the sky). When they collectively exit the tunnel at 30:01, they are still on the New Jersey side, as evidenced by the toll booth clerk who witnesses their flyby. While both the entrance and exit scenes are physically in the same a place, a large American flag was either pasted into the entrance scene or edited out of the exit scene, creating a slightly different visual element to two otherwise identical landscapes.