Continuity mistake: When they finally arrive at the bottom of the sewer, Eddie's bandage is on a different cheek. (01:59:00)
Audio problem: After the aeroplane crashed, a dinosaur stepped over it and the windows shattered making the typical sound of made-of-glass things when broken. They are made of plexiglass (a sort of fibrous plastic).
Factual error: Fitch, who professes qualifications in biology, genetics and biochemistry, says that they made Sil female because she's a natural predator and so she'd be more docile. He should retake his finals. In every single species of predator on earth - every single one - the females are the hunters, aggressors and killers. The males may be socially dominant but they are the 'docile' ones. There are no exceptions - and no human DNA was used to create Sil - they used synthetic DNA based on the instructions transmitted to them.
Revealing mistake: In one shot when the boat is pulling away from the waterfall, you can clearly see that the shot is the same one they used earlier in the movie. The water from the waterfall now is going up the cliff! They have just put it in reverse.
Continuity mistake: If you look carefully at the monster (Frankenstein) you will see that his face is different in the ending scenes. The reason is, during the movie you see the monster take the woman doctor and throw her out the laboratory window. You then see the monster kind of stumble, which he really did and broke his ankle. So in the final scenes they replaced Lon Chaney Jr. as wolfman with a stuntman, and Lon Chaney Jr. finished the movie as the monster.
Continuity mistake: In the British Museum, when Rick and Ardeth are saving Evie, Rick gives her a .45 pistol and they start to shoot the guards, her pistol fires once and the slide locks back meaning the pistol had no ammo, but she keeps firing as if the magazine was still full. (00:39:47)
Factual error: Gorillas are almost exclusively herbivores. They have been observed eating small insects and grubs but nothing larger. So why does Isabelle eat a rat at the beginning of the film? The serum may have turned her into a crazed killer, as it does with Sebastian, but it hasn't changed the structure of her teeth and palate, biochemistry of her digestive system and so on, all of which would be required. She might kill or torture the rat, but she'd never eat it.
Other mistake: In the slaughterhouse scene, after Harrigan has injured the Predator with his shotgun and Keyes reappears, the Predator throws its disc, and severs Keyes in half at the waist. We see his legs flop to the ground, and blood pour from above, but his upper half (torso, backpack and weaponry) mysteriously remain hovering out of sight. (According to the director, the MPAA made him cut the footage of the top half of his body hitting the ground because it was too gory, creating this odd error). (01:21:50)
Factual error: Eddie specifically tells the gang not to take his mom's "Delicious Deals" snacks because his mom loves them. But Delicious Deals are made by Mrs. Freshley, a company that was not founded until 1994. The boxes used in the movie even include the modern design that can be found today in most Dollar Tree stores. (00:23:00)
Continuity mistake: He cuts a hole in her pants for insemination. When in the car moments before fighting the dog there is no hole.
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)
Plot hole: Spoilers. It's revealed that the barn game takes place at an old farmhouse owned by the family of Jill Tuck - Jigsaw's widow. It's public knowledge that she was married to Jigsaw and that buildings they owned served as the headquarters of several past traps, so the barn should have been investigated at some point in the meantime. Ten years have passed. It makes no sense that the barn was never investigated and that the bodies of the barn victims were never discovered.