The opening scene in which Alice is naked in the shower shows her with no makeup. Yet, upon wearing the red dress she is wearing red lipstick. Then, in subsequent shots she is wearing no lipstick again.
During the crow scene when the flamethrower is about to incinerate Carlos, the woman he is holding has her hand on his shoulder. When we cut to Alice in the next shot we can see the woman's hand slide down off of Carlos' shoulder and then reappear there in the next shot.
Towards the end when Alice enters the Umbrella HQ and releases a clone of herself from the water/orb, the clone then dies. She is shown laying on the ground with her left hand covering only her left breast, with her elbow resting on the floor. In the next shot, from above, her arm is covering both and her elbow is no longer resting on the ground.
In the beginning of the movie, the first Alice clone is in a laser chamber where the pattern of the lasers that charge after her are diamond, but then a shot later when she climbs through an air duct, the laser pattern is just a straight line.
After Alice infiltrates the Umbrella facility and prematurely releases one of her clones from stasis, the dead clone is seen from one angle covering its left breast with its left hand. After an immediate cut, the left hand is then seen draped across its body covering its right breast.
When Alice shoots "Stevie" through the head with an arrow, there is blood splatter on the truck after he is hit. After checking the pumps, Alice looks at him a second time and the blood splatter has vanished.
During the Vegas scene, the laptop in the Umbrella tent is locked on to Alice, yet there's a display box containing Africa in the lower left corner. There would be no logical reason for the Umbrella operatives to keep a look out on Africa when they're busy with Nevada.
After the Alice clone is killed at the beginning, her body is shown being dumped into a pit with the other dead clones. Even though Dr. Isaacs has been killing the clones for weeks, none of the dead bodies show any decomposition, nor have any of them desiccated (dried out) in the desert heat.
In the council chambers, Wesker's glasses reflect the room around him. This isn't a mistake - all council chambers are identical, and Wesker's holographic cameras would pick up the reflection of his table - as well as the reflections of the other holograms in the room during a meeting.
After Alice uses her powers to kill the crows, Dr. Isaacs uses 3 satellites to locate her - as evidenced by the display on his computer monitor. Three smaller circles, presumably satellites, centered around a larger circle, presumably the radius of her psionic ability - even though we only see one satellite in orbit. Even if the satellites are not sensitive to psionic bursts (though they should be, since the AI in the Umbrella facility claims to have detected them), Project Alice has several implants which allow Umbrella to track and control her.
At the start of the final scene in Tokyo, there are rats in the street. As the camera descends through the street, one of the rats actually goes in front of the ground revealing that the street is actually a cut-away set.
In the last moments of the film when the camera pans out showing the many clones of Alice. The footage of the awoken clone in the bottom left can be seen reaching the end of the recording and then played in reverse to fill a few extra seconds.
When Dr. Isaacs is held in a "secure room" the keypad used to release the door is quite clearly that of a cheap digital safe (the sort one would buy for keeping a few household valuables) and no attempt has been made to conceal the circular handle of the safe, the rest of which has been built into the wall.
During the scene where Alice comes across the empty gas station she aims her cross bow at the attendant zombie "Stevie" using a basic reflex sight on the bow yet in the scene it shows that she has managed to magnify all the way up to his chest revealing his name. The sight used on the crossbow does not have anywhere near that amount of magnification.
The goof items below may give away important plot points.
When the bus gets attacked by the crows Ashanti's character Nurse Betty has blood and dirt on her face. But after she locks the back door and she shoots the crows she is clean and there is no blood or dirt on her, then in the next shot when she dies she is bloody again.
In the scene where Carlos is in the big rig lighting up his joint, the camera pulls back and you can clearly see that one of the zombies reaching in for him only has makeup just past his wrist where you can then see normal human skin between that and the sleeve of his clothing.