In the first two films, the Red Queen was said and shown to have been based on Angela Ashford. In this film, it's said she was based on Alicia Marcus.
In the second film Dr. Ashford is the one who created the T-Virus.
In the first two films, the Outbreak at the Hive was the first known source of T-Virus zombies, due to the actions of Spence and the Red Queen. (However, in this film, the creation of zombies was an accident as a child infected with the virus died and reanimated, killing the passengers of a skylift car.)
The Red Queen says the Hive Outbreak happened a decade ago. However, as Afterlife said the outbreak began 4 years ago. Unless six years passed since Retribution, it's likely this is an oversight.
The film reveals that Dr. James Marcus was the founder of Umbrella and the creator of the T-virus; Marcus was eventually killed by Wesker under orders from Isaacs. This is an adaptation of James Marcus, the main antagonist of Resident Evil 0, who is also killed by Wesker.
Unlike the games, where Marcus' experiments were unethical and dangerous, the film version of Marcus developed the T-virus to cure his dying daughter, Alicia, who would later be cloned into Alice.
The military vehicle Alice uses to escape the Kipepeo is a BSAA designated vehicle, as seen on the hood and doors. It bears striking resemblance to the military vehicles used by the BSAA in Resident Evil 5.
The Lighter Claire uses to create the improvised explosive to escape from the plastic prison cell looks just like the Lighter from Resident Evil 2 and 3.
When Alice escapes from Isaacs' tanker, she gets into a knife fight with Isaacs on the tanker's roof. This is adapted from the knife fight between Leon Kennedy and Jack Krauser in Resident Evil 4.
Alice escapes the tanker using a motorcycle, and Umbrella's forces attack her from the tanker. This is adapted from the motorcycle chase featuring Jake Muller and Sherry Birkin in Resident Evil 6.
When Alice's group infiltrates the Hive, Wesker initiates a protocol to unleash a horde of Cerberus, prompting the team to run for the Hive. The Cerberus stop their pursuit once the survivors enter the Hive's premises. This is adapted from the opening sequence of Resident Evil, where the S.T.A.R.S. team encounters the Cerberus and must run to the mansion for shelter, where the dogs stop pursuing them.
The bioweapon that kills Razor and fights Alice in the Hive is the Bloodshot from Resident Evil 6.
Doc's role in the film is similar to Wesker's in Resident Evil.
Doc is the leader of the group of survivors in Raccoon City, but he is really working in secret as an informant for Umbrella. Alice deduces that he is the traitor.
In Resident Evil, Wesker is the leader of the S.T.A.R.S. Alpha Team, but is actually working for Umbrella and deliberately trapped the S.T.A.R.S. team. Clues scattered throughout the game reveal Wesker's association with Umbrella.