Factual error: How is it that when Sly comes out of the freezing, icy water, his hair and clothes are bone dry? I don't know too much about hypothermia, but I would imagine that his fairly thin sweater isn't wind proof. I'm sure by the time the movie ended, he would be suffering from more symptoms of hypothermia other than chattering teeth.
Factual error: John Candy is at the top of the Calgary Tower having lunch. In the background you see a building called Bankers Hall which is slightly higher than the Calgary tower, that's fine except this was the 1988 Olympics, that building wasn't completed until late 1990.
Factual error: In the early scene where Dennis Nedry meets a man to plan the embryo theft, the subtitle says that they are in San José, Costa Rica. However, the sleepy coastal town in the movie within sight of the ocean bears no resemblance to the real San José (a cosmopolitan capital of almost 1 million people, situated 50 miles from either coast). Even the book makes this error. (00:13:10 - 00:14:45)
Factual error: Not long into the film, D'Artagnan jumps in some hay. There's a flag of the province of Québec (Canada) visible in the background. This film is set in France at a time this flag didn't even exist.
Factual error: Most of the time the boys have no visible breaths, even though they're in a freezing climate.
Factual error: The movie feels the need to justify the fact that everyone in 1603 Japan happens to speak English (something most kid movies just gloss over) by explaining that they are trading with Great Britain, and therefore the locals picked up the language. That's real cute, but also blatantly false. Trade with the British empire was rather sparse, mostly with Dutch mediation, and knowledge of the English language was practically nonexistent - here, any peasant and even kids are practically bilingual.