For example, the novel claims that the Iron Throne is a splinter group of the Zhentarim (which explains why Montaron and Xzar answered to Sarevok even though they were Zhentarim agents), as opposed to the game who says the Zhentarim and Iron Throne have no connections whatsoever. But the 3e D&D sourcebook "Lords of Darkness" validates the game's lore about the Zhentarim as canon over the novel's, confirming that the Iron Throne is no splinter group of the Zhentarim or any other organization.
And Baldur's Gate never had a Grand Duke by the name of Angelo (The guy who was a corrupt Flaming Fist officer working for Sarevok in the Baldur's Gate game is a Grand Duke in the novelization), the sourcebook Volo's Guide to the Sword Coast which details the Sword Coast lore a couple years and less before Baldur's Gate confirms there was only Belt, Liia, Eltan and Entar as the Grand Dukes.
In Baldur's Gate 3, there is a mural in the Druid enclave that details the history of the druids in the Sword Coast, who worship Silvanus. The final mural hints the Druids' alliance with the Harpers, which also allude to the fact that Jaheira was a Silvanus worshiping Druid working for the Harpers. In the novelization, Jaheira was NOT a druid who worshiped Silvanus, she worshiped Mielikki, which corresponds to the game's lore, but contradicts what what the novelization has.
