Plot hole: Caine's skin becomes visible when it chars, for no reason consistent with the other invisibility. Further, it drops off in an impossible way (since there's no indication the invisibility otherwise changes metabolism/healing). Caine acts far too healthy for someone so severely burned. Finally, the extreme damage to skin and muscles that this implies is not seen when he becomes visible. (Even if the material flaking off is clothing, most of the arguments still apply; burned clothing would adhere to burned skin, and would provide little to no protection from the fire.).

Factual error: An electromagnet is used to pull a metal lever on the other side of a metal door. The metal door would shield the lever, making this impossible.

Continuity: When Kevin Bacon's invisible character shoots another character in the chest with a dart, the dart changes position. First it is on the upper left side of the chest, then it is in the exact centre.

Continuity: In the end of the movie you can see that the doors of the elevator are almost closed. But in the next scene when Linda shoots him with the flamethrower, the doors are open again.

Continuity: When Dr. McKay pushes open the freezer door, she is standing behind the row of wires still connected to the door. A moment later, without moving, she is on the other side of them.

Continuity: When Kevin Bacon gets up and the sticky sensor things rip off his body, they snap backwards and disappear into thin air.

Continuity: In the scene where Linda tapes up Matt's wound, she is seen pulling a large strip of duct tape almost all the way across his stomach. Later, when they first start climbing in the elevator shaft, Matt's shirt rides up and the tape is gone.

Continuity: When Linda and Matt are trying to escape from the freezer, the amount of blood changes on the door lock.

Other: When they put the reversal liquid into the ape, a rubber band was used to help find the blood vessel. When they did the same thing for Sebastian, no rubber band was used but they were quickly successful at finding the vessel.

Continuity: Matt is bitten by the gorilla on his hand in the beginning, but in the next scene where the gorilla is strapped to the table, his hand is fine. Shortly after the gorilla is made visible, his hand is suddenly bandaged.

Factual error: Duct tape would not stick to bloody skin at 40 below zero, and probably not at higher temperatures either; again because of the blood.

Visible crew/equipment: When Sebastian is stalking his neighbor and looking at her to see if he can see her undress in the beginning, there is a brief moment where you can see the reflection of a camera crew in the window looking into Sebastian's apartment.

Continuity: When the team tries to make Caine invisible, he tears off all the sensors and wires from his chest. Yet the surrounding machines continue to display his heart rate and blood pressure.

Continuity: When Elizabeth Shue sets off the automatic sprinkler system on the ceiling, a great amount of water is spraying from each one. However, after Shue and Josh Brolin attempt to climb up the escape ladder through the elevator shaft all that water is gone, where did it go?

Continuity: When Sebastian goes to Linda's apartment to catch her and Matthew together, we see Linda welcome Matt by pulling her jeans down. Matt picks her up, hands on her bare butt. After he carries her into the bedroom, Sebastian throws a rock through the window and we see them on the bed, her jeans are pulled back up to her waist. Not the direction clothing usually goes in such situations.

Deliberate "mistake": Elizabeth Shue uses a drawer handle as an electromagnet. OK if it's really a magnetic material but lab furniture is generally made of aluminium or stainless steel which is not. There is no way that they would use an iron handle in a potentially wet, and hence corrosive, environment such as a freezer.

Deliberate "mistake": When Sebastian goes to his employers house to kill him, the man is standing by his pool smoking a cigarette. When the boss blows smoke in Sebastian's direction, Sebastian appears and scares him. Since Sebastian is invisible you shouldn't be able to see his pupils, only an outline of his eyeballs, but you can see the pupils.

Other: After the veterinarian throws blood all over the floor, we see clean spots appear on the floor in the shape of Sebastian's feet as he walks through the blood. Somehow he never has any of it stick to the bottom of his feet (even when he's in the puddle).

Continuity: In the early part of the movie when Sebastian is checking the stability of the molecule, you see the 3D molecule model explode and the separated atoms pause. When Sebastian turns away, you can see that the atoms are no longer on the same position.

Continuity: When the redhead spilled the blood all over the floor to see if he was coming at her there is a little area to the left of the screen he could walk on without her seeing it. The next shot it's gone.