When Charly has one of her first flashbacks she sees Timothy and Jack from the vantage point of the trunk of a car. It is 1988. Timothy says, "She's the Energizer Bunny." Unfortunately the bunny didn't exist until 1989.
During the scene in the train station, Charly has a beer at
the bar. When Timothy begins to speak with her, an orange mic (and extender) are visible in the lower right-hand portion of the screen. You can see it in two different shots. It is present on the DVD and the video.
During the climactic knife fight with Timothy, Charly is slashed on her right side ribcage. Later, when Charly is lifting herself on the rope mesh, the wound has moved to her left side and appears to be more of a puncture, rather than the long slash she had received originally.
In the water mill house, the actions used to raise and lower the water wheel change. For example, one moment the water wheel is lowered by turning the crank clockwise and the next moment the wheel is lowered by turning the crank counter-clockwise. Similarly, Daedalus first raises the wheel by turning the crank clockwise and then moments later raises it using a counter-clockwise turn of the crank.
During the scene when Sam is first cutting the carrot, she is shown cutting with two separate motions, depending on the shot. Generally, in shots where only her hands are visible, she is cutting by pivoting the knife against the board, raising and lowering the blade at the rear; in long shots, she is chopping by swinging the knife up and down from her wrist, raising and lowering the point.
Charly breaks free from her frozen prison by blowing off a heavy metal door. We see that the explosion bursts through at least two ceilings. Between the explosion and the ensuing crater, it seems highly unlikely anyone upstairs could have survived - or for that matter, left the basement through all the rubble.
Kerosene does not ignite at sub-zero temperatures and since it sat on the floor of a freezer for several minutes it's temperature was definitely below the minimum temperature requirement. Additionally, the fumes would have fully dissipated in the time frame shown in the movie, further hindering ignition.
There is no reason to have a water mill wheel controlled by a hand winch, except as a movie torture device. The traditional purpose of such a wheel is to derive power from the flowing water, and supply it to some mechanism (such as a grain mill or saw mill). Not for some mechanism to spin the wheel through the water.
A knife thrown horizontally cannot embed in a horizontal surface, such as a chair seat. It would bounce off and continue moving horizontally until it hit a vertical surface, such as the person in the chair.
When Caitlyn gets Charly back on her feet, a shot of the bomb timer shows 4:59 (four minutes, fifty nine seconds) to go. However, the explosion happens 3:46 (three minutes, forty six seconds) later. This is not a mistake since the countdown does not necessarily occur in real time.
A call is traced to Niagara Falls. 716 is the area code for Niagara Falls. However, the film clearly shows that the receiver (Charly) is on area code 315 while the caller (the one they are tracing) is calling from number (716) 555 1304, which is indeed Niagara Falls area code.
After driving the tanker truck through town, Charly comes on a downgrade with a car in front of her. She pumps the brake pedal and it shows brake fluid leaking from a cut line. Tanker trucks (big rigs) do not use hydraulic fluid in their brake systems, they all use compressed air to release their brakes. So a leak causes the brakes to stop the truck.
Immediately after you see Charly perform a "hockey stop," the camera pans up to her face. The bag on her right hip pops into existence. It is obviously someone else doing the skate-work and a cut to the actress Geena halfway through the pan.
In the bridge scene, when federal agent with walkie-talkie throws himself off the path of Mitch's car, the agent's fall trajectory is obviously altered in compositing software in order to appear he covered more distance. Also, the layer of his green-screen footage suffers artificial deformations at the moment his body touches the pavement.
As Mitch and Sam talk in the car on the way back to her house, the windshield wipers obviously miss sweeping part of the windshield which is free of snow, revealing the white mask on the glass to be paint, and the falling snow to be fake.
The goof item below may give away important plot points.
Errors in geography
When Charly is walking through Atlantic City, before gets led into the alley by the headhunter, (right before Mitch says his line about the gun not being a ham on rye,) a light up sign for a store called Honest Ed's is visible in the background. This is a rather famous store located in Toronto, Canada.