Sil has a tan line, contact lenses, and pierced ears, all of which she could never have obtained within the movie's world.
Sil is in the process of removing the swimwear from the "hot tub guy" when the good guys show up to get her. But after she notices they arrived for her, the swim short on the guy seems to have been pulled back up to the guy's waist.
The alien's son at the end of the movie is circumcised. Having just been born, and not having the ability to immediately follow quaint US customs, he probably should not have been.
When Preston Lennox (Michael Madsen) and Dr. Laura Baker (Marg Helgenberger) are kissing while she's leaning against the door to her hotel room, her bathroom can be seen through a doorway to her left. At the same time, Sil (Natasha Henstridge) is shown in the hallway listening at the door. To *her* left (both characters are facing the same direction, they're just on opposite sides of the same door) is the door to another hotel room, instead of a wall that the bathroom would be on the other side of.
The Porter on the train is a rather large lady. Yet her uniform almost perfectly fits Sil when she leaves the train.
Correction: The conductor's uniform is actually a very bad fit on Sil, just as the coat she takes from her first lover. And the clothes she initially steals before the cocoon. Besides limited choices, Sil doesn't really understand how to dress - only that she's covered.
The conductor gets half-sucked into the cocoon, resulting in her death. Sil later emerges from the messy cocoon, covered with its fluid and falling right on top of the conductor. But when Sil dons the conductor's clothes, they are spotless.
When the scientists try to kill young Sil they flood her cell with what is supposed to be cyanide gas. That gas looks like white steam, whereas Cyanide gas is invisible.
When Sil ditches the BMW, a police officer finds it later and looks inside. It appears to be out of petrol, but the fuel gauge goes from R to F instead of E to F. However, fuel gauges on BMWs (like most European brands) are labeled "R" for "Refuel" to warn when the fuel tank is depleted. Gauges bearing "E" for "Empty" are customary on American and Japanese marques.
When the team assembles for the first time and Ben Kingsley explains the signal from SETI, he looks straight into the camera - twice.
When Sil crosses the street and the car brakes sharply, the horn is heard, but the driver's hands are all the time on the steering wheel, so he wasn't pressing the horn.
Dressed in black, pushing a dummy out of the car that is speeding down the hill.
When Sil walks around the streets of Los Angeles in her new dress, one shot reflects a white crew van driving past a store window and filming. Likewise, the cameraman's shadow can be seen on a few extras as they walk past Sil.
Reflected on the vintage red Mustang as it stops at the sight of Sil's accident.
As Sil exits the BMW due to a lack of gas, swinging the car door open, several crew members are reflected in the wing mirror.
The team goes back to the hotel, and after having drinks they go to their rooms. A member of the hotel staff is seen knocking a door, saying "Housekeeping" and Sil then obtains her keys. However no-one would be making housekeeping rounds in the evening.
Visible in the reflection off the glass patio door when Robbie brings Sil back to his house.
Shadow, on the train compartment, above Dan's head.
Despite dealing with emergency services, hospital staff, hotel staff, etc., at no point are Fitch nor any of his team asked what their authority is for requesting information, surveillance tapes, etc., nor do any of them appear to be wearing any kind of ID.
When young S1L is about to transition/cocoon after her nightmare, she cries out in pain and says "Oh God!"
As she had been in complete captivity up to that point, there is little chance she would have any concept of God, or the context in which she was using it.
Through the entire movie, Lennox has been using a Glock 19. Yet when he is shooting at SIL after he uses his knife to free himself from her, "Breast Tentacles," he is clearly firing a Beretta 92FS.