While Clavell conducted extensive research on Japanese history and culture to provide a rich and immersive setting for the novel, there are several elements in "Shōgun" that deviate from historical accuracy. Some of the areas where the novel may not be entirely historically accurate include:

1. Characters and Events: Many of the characters and events in "Shōgun" are fictional or loosely based on historical figures. For example, the protagonist John Blackthorne and other key characters are entirely fictional, and while some historical figures such as Tokugawa Ieyasu, the powerful daimyō of Japan, are mentioned, their portrayal and actions may not always be historically accurate.
2. Cultural and Social Customs: While "Shōgun" provides insights into Japanese culture and society during the 17th century, some of the customs, traditions, and practices depicted in the novel may be fictionalized or exaggerated for dramatic effect. Clavell's portrayal of Japanese customs and society should be approached with caution and not taken as entirely accurate.
3. Language and Dialogue: The novel is written in English, and the dialogue between characters is in English, even though the characters are supposed to be speaking in Japanese. This can result in a loss of linguistic accuracy and cultural nuances, as the original language and dialects spoken during that time period may have been quite different from how they are portrayed in English.
4. Plot and Storyline: "Shōgun" is a work of fiction with a complex plot and storyline that may not always align with historical events. Clavell takes creative liberties to develop the narrative and may deviate from historical facts to suit the needs of the story.