When Sinclair's car is hit by the red SUV, in the shot shown just after the first ramming there is no damage to the SUV or the FBI car. No damage is seen to the cars in several exterior shots until the second ramming when Sinclair loses control. Interior and exterior shots of the crash do not match.
When Charlie encounters Larry, he asks about the set of knotted strings draped around his neck. Larry refers to it as an "Aztec quipu" and says it was used in Tenochtitlan (the capital of the Aztec empire). Quipus, however, were used by the Incas of the Andes Mountains of South America, not the Aztecs of Mexico. A few hundred survive, but have not been definitively deciphered. It is thought that quipus encoded both numeric and verbal information, but a majority of the data examined so far appears to be numeric.
Charlie and Amita look up, apparently seeing the Space Shuttle re-entering the atmosphere. They then run inside to watch the landing on TV. Furthermore is is mentioned the Shuttle is landing at Edwards Air Force Base in California. First, it takes about half an hour for the Space Shuttle to reach the ground after reentry. In addition, if the Shuttle plans to land in California it re-enters several thousand miles west of California. It would not have been possible for anyone in California to see the re-entry.
While Pony thrashes around on the FMRI table the supposed image of his brain remains unmoving on the screen.