It was briefly stated in the second film that the T-Virus was created by Dr. Ashford to cure his daughter Angela and that the Red and White Queens were based on her. This movie contradicts that by suggesting that Dr. Marcus created the T-Virus to cure his daughter Alicia, and that the Red/White Queens were modeled after her. While the rest of the movie stays true to the continuity of the previous films, this rather obvious ret-con is still a major continuity gaff.
Every previous film ended with a dramatic zoom-out starting with Alice that teased the events of the sequel that followed. Appropriately, "The Final Chapter" ends by doing the opposite - dramatically zooming into Alice and ending with an extreme closeup of her eye. This also bookends the series, as she was introduced in the first film with an extreme closeup of her eye opening.