At the beginning of the movie, Alice gives a history of the Umbrella Corporation. She says that the T-Virus was created by a Dr. Marcus for his daughter Alicia to prevent her rapid aging. This completely contradicts the story of Resident Evil: Apocalypse as this movie establishes the T-Virus as being created by Dr. Ashford for his daughter Angie. While the novelization explains that Dr. Ashford created the Virus at the behest of Dr. Marcus, this is never made clear in the film.
In Resident Evil: Extinction (2007) it is stated that Dr. Isaacs is under Albert Wesker commands, but in this new installment Isaacs is in charge and Albert Wesker is just an employee.
(at around 16 mins) When Alice is driving to to Hive, and her car runs over a spike strip, and then under a tractor trailer which rips the roof off of the car - the next scene shows the car crashing into a telephone pole. The scene where it hits the pole, the roof is still on the car, next scene it's gone, then next scene it's back again with telephone pole wires landing on the car, and then it's gone again as Alice exits the car.
The Final Chapter supposedly takes place 10 years after the outbreak in Raccoon City, but this is impossible. Resident Evil (2002) takes place in 2002 with Resident Evil: Apocalypse (2004) taking place only a day, or at most a few days after the first. Resident Evil: Extinction (2007) takes place 5 years after the first outbreak putting the time line at 2007. Then Resident Evil: Afterlife (2010) takes place 18 months after Extinction placing it most likely in 2009. Then _Resident Evil Retribution_ takes place directly after Afterlife and the Final Chapter takes place 3 weeks after Retribution. That would mean that only 6-7 years have passed since the outbreak in Raccoon City, not 10.
At the end of the air intake scene, Alice stares at the cc camera, but on the next take, on her screen image, she looks above it instead of staring right into it.
(at around 8 mins) Alice has trouble starting a Humvee, however military Humvee (such as the one she is starting) are not, and never have been operated by turning a key into an ignition.
The Reflecting Pool, the shallow pond which faces the Lincoln Monument, is refreshed by the National Park Service. Since the world has been destroyed it is likely that there would be no one to service the pond and therefore it would be dry. Furthermore, Alice would have become seriously ill after drinking from this stagnant pond, much less one in which a rotting T-virus victim was hiding in.
(at around 20 mins) When Alice meets the clone Isaacs in the Umbrella Tank she states that she was the one who killed the original Isaacs, when in fact it was her clone that killed him using the laser grid.
The survivors note a second wave of undead heading towards them. They look through a thermal scope at a huge blob of red (indicating the horde). The dead do not give off thermal energy and would not show up on a thermal scope.
Given that Raccoon City was destroyed by a nuclear missle strike, there is no way that the ruins would be habitable enough for an entire convoy of survivors to take refuge in there. For context, the city of Pripyat is still harboring dangerous levels of radiation decades after the Chernobyl disaster, so there's no way the survivors can be hiding in the ruins of Raccoon City only a decade after its destruction and not experience toxic levels of radiation sickness.
When Alice arrives in Raccoon city, a scene shows the devastated city. On the right, a plane wreckage is seen with smoke rising. Considering the time interval between widespread of virus and the movie events, the plane crash would have happened years ago and the smoke would have ceased long before the movie takes place.
(at around 27 mins) Dr. Isaac's clone gets his hand cut off. The stump gets covered with an elastic material. The shape of a fist is clearly visible beneath it.
Young Alicia / Red Queen has a mole on her cheek. It keeps switching sides.
(at around 1h 35 mins) In the last scene of the film you can clearly see the completed One World Trade Center Tower in the background. In the first 3 movies in the series it is specified that the T-Virus Outbreak occurred in 2002 and much of the world population was wiped out in that year. The tower should not exist.
(at around 8 mins) Washington D.C. is a former swamp that rises to low hills on its northern, western and eastern approaches. When Alice is fleeing the T-virus flying the flat area in which she is driving clearly is not Washington and its environs, ruined or not.
(at around 1h 30 mins) There is no way that the "real" Isaacs could catch up to Alice and catch the vial of Anti-virus when she drops it. He would have had to be riding the elevator up from the Hive with Alice.
(at around 1h 12 mins) The bag left by the original team that entered the Hive in the first movie shows no wear or dust from being left in the same position for 10 years when the Laser Grid hallway is covered in muck.
The White Queen explains in Resident Evil: Extinction (2007) that Alice's blood could potentially be used as a cure for the T-Virus because she is resistant to its negative effects and bonded with it. This plot point is never mentioned again, nor does it seem to be connected to the airborne anti-virus that is a part of this film's plot, which is established to be guaranteed to kill anything infected with the T-Virus.
As revealed in this film, Alicia Marcus was who the T-Virus was invented for in the first place, to cure her progeria. This calls into question the plot of Resident Evil: Extinction (2007), where Isaacs keeps cloning Alice to figure out why the T-Virus bonded with her so well. Wouldn't it be fairly obvious to him and the rest of Umbrella that the reason why it bonded with her so well was because the T-Virus was designed for Alicia in the first place? Alice is a genetic copy of her after all, biologically identical.
Dr Isaacs and Wesker becomes suspicious of Alice knowing of airborne antivirus. And yet, they bring her, who is a strong adversary, to the facility where the antivirus is held. It would be wiser to take her further to prevent her to reach the cure within time.
Alice detonating a bomb inches away from the vial of anti-virus that is in Isaacs' coat pocket is extremely careless, as it could have easily destroyed it and everything she was trying to protect.
To drive the undead away, Alice and friends tie an enemy soldier to the back of the vehicle and let it go. The zombies begin to chase the bait, but none attack the 4 or 5 people who sent the bait.
Alice stating that the American government sent the nuclear missle to destroy Raccoon City in the opening recap directly contradicts the events of Resident Evil: Apocalypse (2004). In that film, it's made very clear that Umbrella is who sent out the nuclear missle strike to Raccoon City, in an attempt to cover their tracks and contain the outbreak while blaming it on a meltdown.
After releasing the female bait, Dr Isaacs orders to shoot her when she's close to the gate, yet he does not order to shoot the two defenders at the gate, just a few feet further than the bait.
Alice takes a motorcycle for her escape. The motorcycle, though not a pure adventure bike, is a dual-sport BMW bike which can also ride in mild rough terrain. For her, it would be easier to get off the road and getting out of Umbrella vehicle's weapons trajectory.