A number of SF books have world building that includes a very important mistake made either before the book starts or as part of the plot. Often this leads to a ship colonizing a planet without needed resources or one that isn't quite compatible with human health, or a misunderstanding starts a war.
One of my favorite mistakes is in Mirabile by Janet Kagan. Someone on Earth thought it would be a good idea to add redundancy to the genes of the plants and animals stocking a generation colony ship. This means that the herd of miniature cows would sometimes give birth to a longhorn, or even a buffalo. Some of the other surprises were dangerous, like the Kangaroo Rex and the Frankenswine, which were vicious. Mutations happen right? And the hidden genes sometimes mutated too.....
One of my favorite mistakes is in
Another superb one was the planetary survey of Pern which missed the fact that thread strikes periodically.
What's a Big Mistake that sticks in your mind from a story?