- Angst? What Angst?: That Angie is nowhere to be seen and nobody ever mentions her is weird, but if we assume the novelization's stance that she died between the events of this film and the previous (because Alice was mind-controlled into shooting her!) and that's why Alice left, then it is jarring that neither Alice nor Carlos seem distraught about it.
- Ass Pull:
- The T-Virus being now able to cause a global drought, for completely unexplained reasons. How does that even work in-universe?
- The fact that one of the Alice clones knows how to use the laser grid (and does it skilfully and just in time to kill Tyrant-Isaacs and save Alice). The clones were made to reproduct an amnesiac, disoriented Alice from the first film, and that particular clone was choking and shaking upon leaving her jar only minutes earlier.
- Awesome Music: For the first trailer, The Crystal Method's "I Know It's You", which included vocals by Milla Jovovich herself.
- Idiot Plot: In a truly bizarre iteration of this trope, Dr. Isaacs becomes bent on capturing Alice in order to use her DNA for his zombie experiments despite the fact that, by all reasonable logic, he should already have her DNA if he can create clones of her (who display the same physical training as her, proving they also carry all her epigenetical baggage). It is never revealed either why does he make all his Alice clones to pass an array of Hive-inspired death traps for, or why is that supposed to be vital for his experiments with her, or how did he expect to recover the original Alice's DNA after the waves of zombies he sent against the survivors had overwhelmed her. To top it off, it's shown that those incoherences are the last thing the Umbrella board is worried about when they learn about them, given that even their spectacular waste of Umbrella's officially dwindling resources is barely addressed.
- Umbrella's board conference has the notable bloop that all the members have physical glasses of water on the table despite they are holograms. A viewer with enough observing skills to notice this might chuckle at the detail.
- The girl calling herself K-Mart because they encountered her in a K-Mart and she felt like changing her name. While this might have been intended to be taken as some kind of coping mechanism for a probable trauma, it doesn't stop it from being rather silly.
- Tyrant-Isaacs proclaiming to be "the future". Considering that, lethal tentacles and psychic powers aside, he looks seriously diseased by his mutation and can barely move around, it is easy to agree with Alice when she laughs at the boast.
- Older Than They Think: As mentioned in Resident Evil: Apocalypse, the similarities between Alice's arc and the 1991 Dark Warrior OVA doesn't end in the previous film. In the sequel to the OVA, the evil corporation the protagonist fights again is led by a scientist in charge of a Cloning Blues project who receives orders from a holographic board of executives, not to count the corporation's head, a sinister, inexpressive blond-haired man who is even more superhuman than the main character. At some point, the scientist breaks away from the corporation and he and his bioweapons have to be put down by the protagonist, who then follows his path of revenge against the corporation. The scientist even looks a lot like Ian Glenn, and the board scene is so similar to the one from this film that it would be shocking that they are not an intentional Shout-Out.
- Rescued from the Scrappy Heap: L.J. drops his Modern Minstrelsy shtick from the last movie and becomes an actual character rather than a "street flava" joke-dispensing device. Unfortunately, it's only then that he gets killed off.
- The Scrappy: This film solidifed Alice's status as such in the franchise due to how her status was taken Up to Eleven. At the end of the film, she has not only essentially made all the characters from the games play second fiddle to her, in no small part due to having psychic powers completely alien to the games, but has also gained an army of clones with her same psychic powers.
- Special Effects Failure: The scene of the mutated Isaacs killing Slater through his eyes and mouth has some seriously bad CGI on it, in contrast with most of the rest of the film.
- They Wasted a Perfectly Good Character: Given that there is a teenage girl in the convoy who gets a lot of screentime, the viewer could be forgiven for guessing she's Angela Ashford after the Time Skip and then getting surprised when she's revealed to be a new character named K-Mart. Had she really been Angie, many interesting storylines would have been possible thanks to her lingering T-Virus mutation and implied psychic bond with Alice (and even although her actress Sophie Vavasseur wasn't available, the mentioned Time Skip would have allowed to recast her believably). Instead, the character of Angela is literally forgotten, and unlike Jill she never reappears or is mentioned again in the franchise.
- They Wasted a Perfectly Good Plot:
- Unlike film continuity, the novelization explains Angie's absence from the film as having been murdered by Alice under Umbrella's cybernetic mind control. Despite being a plot point that would have produced a great lot of drama and could have been used to give Alice more depth, nothing of this is used in the film proper, as Alice and Carlos are positively cheerful in their reunion and never dedicate a word to their vanished friend.
- The goal of Isaacs's simulations with the Alice clones is oddly never explained: he just says he is using their blood to try to make docile zombies, but that doesn't explain why he needs the clones to overcome the original Hive's obstacles. It's inevitable to think that, if the producers were going to include Cloning Blues and callbacks to the previous installments, they could have created many possible interesting plots instead of just because. (This is admittedly exploited in Resident Evil: Retribution, but still very superficially.)
- WTH, Casting Agency?: Jason O'Mara was disliked in his short role as Wesker, making people somewhat relieved when he was be recast in the next installment.
YMMV / Resident Evil: Extinction