Jossed: Resident Evil 3: Nemesis contradicted many plot elements that were present in other media tie-ins such as the S.D. Perry novels and the Biohazard 2 audio dramas that were produced by Flagship (the same company that wrote Resident Evil 2). Particularly, the cause of Raccoon City's destruction was changed from a fire that spread across the entire town to a nuclear missile launched by the U.S. government.
Urban Legend of Zelda: There used to be a persistent fan rumor that Nemesis was secretly one of the series' pre-existing characters who was captured and mutated by Umbrella (this was mostly due to a mistranslated interview with one of the Resident Evil developers that wrongly implied he was supposed to have been a significant character before). They ultimately ended up using this angle with his character in the movies.
What Could Have Been: Two Resident Evil games were in production during the time of Resident Evil 3's development. The official RE3 was one of them. The other one would have featured a private investigator named Tony Redgrave as the protagonist, and its development included several trips to Spain to study castles as inspiration for the environments. If any of that sounds familiar, then that is because this game was retooled into Devil May Cry after being deemed too great a departure from the Resident Evilsurvival horror formula.