Factual error: Flynn says that the chamber in the Mayan temple is "an exact replica of their great temple of Teotihuacan." But Teotihuacan was not a Mayan city, but rather the hub of a separate civilization (themselves called the Teotihuacan). It was in central Mexico, hundreds of miles from the Mayan area in the Yucatan Peninsula.
Factual error: Flynn says that the chamber in the Mayan temple is 300 quahuitls long. A quahuitl is approximately 2.5 meters, so 300 quahuitls would be 750 meters, or nearly half a mile. The chamber he and the others are in is large, but not that large.
Factual error: When Flynn presses the stones at the Mayan temple, he identifies the numbers that are carved on them. The stones do have the bars and dots of the vigecimal Mayan numerical system. However, he identifies the specific numbers incorrectly. For example, the stone that he claims says 65 actually has 180 imprinted on it.
Factual error: Flynn gives the size of the chamber in the Mayan temple as "300 quahuitls by 20 quahuitls." But the quahuitl was an Aztec unit of measurement, and was not used by the Maya. (01:06:00)
Factual error: In the beginning the professor says that they have now built a 1:20 scale copy of the great pyramid including capstone. In the final fight, the pyramid contains a huge room inside - in the full height of the pyramid. But the Egyptian pyramids are (almost) solid.