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 the Senator is about to be sacrificed, the cloth on her mouth immediately disappears for a split second. (01:29:35)
Factual error: When they are trying to navigate the shuttle through Eadu, the shuttle abruptly collides with a rock, which causes Bodhi to jolt backwards. If the shuttle hitting the rock had caused the shuttle reduce speed so abruptly, in the way that was shown, then Bodhi would have jolted forwards, not backwards. (00:57:05)
Character mistake: When Tris and Christina are going to rescue Four, Tris asks how to use the drones. When Christina tells her that she must use her left hand she can be seen using her right hand to control them.
Continuity mistake: As Captain America arrives in his car at the airport car park, he stops right next to the line dividing the spots. In the following shot, when he steps out, the car is further away from the line, more towards the center of the spot. (01:26:50)
Factual error: The EMP burst would have only affected a small number of vehicles. Most vehicles act like a Faraday Cage.
Other mistake: Just before Patricia Whitmore's plane (no. 107) is shot down, it is briefly shown with its number mirrored.
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)
Character mistake: When the elder Vulcans inform young Spock of the death of the older Spock, they show him a tablet that has him listed as "Second Officer - USS Enterprise." Spock was First Officer.
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: At the mansion, the tour guide hits the square on the wall twice.
Plot hole: The system providing oxygen can only be accessed by someone slim. Therefore John Goodman built the bunker with him unable to access the key facility that provides oxygen in his bunker. Yet he must have been able to go and get Britney when she went to that area?
Suggested correction: It's not a plot hole because he said in the film, the normal hatch to the air filtration was blocked by something that fell on top so they couldn't get through that way.
Continuity mistake: The chef at the airport stabs someone, but the knife blade is clean afterwards; moments later he stabs it through the valise, and it is covered in blood.
Continuity mistake: Throughout the movie, fire axes seem to be the weapons of choice. Only two fire axes are used, but they appear recurrently. In the very first use, the protagonists grab fire axes to butcher the monster called Beverly. Blood and gore go everywhere; yet, the axes emerge from this bloodbath with no blood or gore on the handles - they're virtually pristine moments later. The axes are used again and again, right up to the ending, and blood comes and goes from the axe handles seemingly at random.
Revealing mistake: When Gabby and Fin are hanging off the building in Las Vegas, you can see that Gabby isn't holding on to anything in some close-up shots. (00:11:47)
Audio problem: In the final conversation between Limus and Bardot, the robotic effect usually applied to her voice is missing.
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)
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. (00:45:55)