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.
Other mistake: When Amy Adams leaves the spacecraft for the final time she is met by Jeremy Renner who throws a blanket around her shoulders. As he does so, the blanket gets caught on something out of view top-of-frame (presumably a boom mic) and he has to tug at it to free it. This was part of one long take in fading light and given the amount of background action going on it was presumably too difficult or time consuming to re-shoot. (01:32:55)
Continuity mistake: When they are at Sarah's house, the boy's father tells her to go outside and ask Lucas to pull the van around back. When Sarah walks to talk to Lucas her long braided hair is tucked into her shirt and her arms are crossed. In the next shot when the camera comes back, her hair is on the outside of her shirt despite her arms still being crossed.
Factual error: The film is mostly set in Moldova. Early in the film, the general remarks at one point that insurgents are near the Russian border to the north. However Moldova does not border with Russia at any point in its geography. It only borders Ukraine and Romania.
Continuity mistake: The gang Bo is reluctantly part of gets to Maurice's crib where he is playing cards with his homies. The red jacketed one is defiant, and grabs a handful of red and blue chips in front of him tossing them in Angelo's face. But if you check out of the table in the wide shots before this occurs, you'll notice that red chips were never in the stack in front of him to begin with. (00:19:05)Sammo