Continuity mistake: 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.
Continuity mistake: When Alice is narrating the previous events, we see the Red Queen appearing. We see her head appear and then the camera changes. In the second camera angle, the Queen's head appears again. (00:04:30)
Continuity mistake: When the armored truck is headed to Raccoon City, there is a shot of 2 cars close together that instantly become further apart. (00:22:50)
Continuity mistake: There is a scene of Alice being dragged by a line behind Isaacs' tank ahead of a horde of zombies. There is no other line next to running Alice. When she climbs upon the tank to attack the guard, another line with torn hands is seen being dragged on the road, where Alice was dragged. (00:21:15 - 00:23:45)
Answer: In all honestly... this film series isn't one to shy away from ret-conning elements of prior films. ("Ret-con" being short for "retroactive continuity" - a storytelling device in which rules and plot-points are either changed or ignored in later installments.) This just seems to be another example of a ret-con. The idea that Alice was the "cure" all along would have ended the series a lot sooner, and they wanted to make more movies, so they just sort-of "ignored" this idea in the sequels that followed "Extinction."
TedStixon