Continuity mistake: The BMW that Sil takes after killing the guy she picks up at the club is damaged on the driver front fender when we see her wake up in it at the beach parking lot. However prior to that the car is undamaged when they leave the club and when it turns into the driveway. We never see how the car became damaged. (00:41:00 - 00:48:00)
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.
Visible crew/equipment: In the scene where she drives the car (with the kidnapped woman in it) down the hill towards the breaker/electrical box, when she hops out at the very last second you can clearly see a person dressed all in black sitting in the driver's seat driving the car down the hill.
Visible crew/equipment: When Robbie takes Sil home, a reflection of a boom mic can be seen on the glass door behind him.
Other mistake: In the beginning of the film when you're introduced to the younger, humanoid Sil in the laboratory, an extreme close-up of her eyes and face clearly reveals the young actor's contact lenses.
Other mistake: When Sil jumps through the hotel room wall, Pres fires two shots from his Glock and then gets in the elevator. In the elevator he drops the magazine and his Glock has the slide locked back showing the magazine is empty. The man is an acknowledged expert in special ops (Indeed, the fact that he changes magazines in the elevator demonstrates his preparedness. He wants to face Sil with every bullet he can, he doesn't want to be even two short.) He is going up against an extremely dangerous extraterrestrial life form that has already killed several people. There is absolutely no way he would be carrying a weapon that was not fully loaded.
Factual error: At the end when the oil in the cavern is burning there is no sign of smoke. With a fire as large as it appears to be, everyone in there should be choking to death, yet they don't even seem the least bit bothered. Forest Whitaker should have also been roasting over the flames, yet he is unscathed.
Character mistake: Xavier is exiting an elevator and turning down a corridor to meet the other agents before bursting in on Sil and the murdered Alfred. When Sil flees it is revealed she murdered the maid to gain access to Alfred's room. To everyone's surprise the maids' dead body is positioned right outside the elevator. Surely Xavier would have seen the dead maid when he came up?