Revealing mistake: When the aqueduct chase has finised, and the T-1000 strolls out of the fire, You can see that the semi is hardly burning in the background. Now, considering that the semi has just violently exploded, and the small bridge it just crashed into was nearly flattened, it seems odd that it shouldn't be burning (very tricky to see, best use zoom in).
Continuity mistake: When John Connor holds the Terminator's jacket up to the light in the shed in Mexico it's full of holes. You see the back of it when they leave (to chase Sarah) and there are no holes.
Revealing mistake: In the scene where the Terminator and the T-1000 are fighting in the corridors of The Galleria, the Terminator has fired multiple shots at the T-1000. When he gets up off the floor, the Terminator throws him into the left wall and the impact hole is already visible before he hits.
Revealing mistake: When Arnold begins to beat up and throw around the workers of the hospital, the African American worker is thrown into a window. If you look carefully you can see that the window he is thrown into is a different kind of glass than the other windows that surround it, indicating that this is not real glass. You can also see that none of the other window frames of glass on the inside of the corridor. There is just the metal frames covering the windows. In some shots later in the scene when the T-1000 is chasing them down the corridor you can see the bits of glass that were left over from before have disappeared.
Other mistake: In the bar fight scene the Terminator gets stabbed by one of the bikers - if you watch carefully you see the rubber knife bend in a few frames.
Visible crew/equipment: Camera lights are reflected in the glass door in the shot behind Dyson as Sarah Connor laser-scopes him.
Continuity mistake: This is during the Special Edition's chip removal scene. There is a point where the shot is of the Terminator's POV. In the foreground a pair of pliers moves vertically through the frame. However, in the "reflection," Sarah Conner is already tinkering with the Terminator's head. Apparently Linda Hamilton (who played Sarah) and her twin sister were out of synch for that shot.
Continuity mistake: When Sarah runs into the corridor to smack the guy with a broom handle, we see a close-up of him having just emerged from a store-room and turned round, standing right next to the door. There's then a very brief shot of Sarah swinging towards him, then a white flash. When we cut out to a wider shot, he's suddenly in the middle of the corridor, with no time to have moved there.
Continuity mistake: As the Terminator and the rest are escaping from Cyberdyne Systems in the police van, the helicopter explodes about five feet before it hits the van.
Continuity mistake: When the SWAT van crashes through Cyberdyne's front doors into the lobby, it comes to rest with the rear doors closed. When Sarah and John Connor enter it, it's in a different position and the rear doors are fully open.
Factual error: In the desert when the Terminator uncovers the cache of weapons, they are stored underground in rifle racks without any protection at all. Weapons are normally stored covered in grease, wrapped in cloth or paper and in wooden boxes. Buried unprotected (even in the desert), a weapons cache would turn into rusty junk in a couple of months.
Visible crew/equipment: In the Cyberdyne lobby when the Terminator walks towards the SWAT team, you can see unexploded squibs (pyrotechnics) in the wall behind him to his left (before the shooting starts).
Visible crew/equipment: In the escape from the hospital where the car is driving fast in reverse, the stunt driver's head is visible sticking up from inside the trunk driving the car from the back. It's too far back to be John Connor's head.
Continuity mistake: When the T-1000 is chasing Sarah, John, and the Terminator in the nitrogen truck, just before Arnie fires the first grenade, a blue car comes between them forming a diagonal line across the road (the Terminator, blue car, truck). After a brief close-up on the Terminator shooting, we cut back to a wide shot, the blue car's disappeared, and the truck's now directly behind him, Sarah, and John; not enough time for them to move like that.
Continuity mistake: In the scene where the Terminator and John are at the pay phone John picks the gun off the floor, it's cocked when it's in his hand, but as soon as he passes it to the Terminator, it's not cocked any more.
Continuity mistake: In the car chase just before the final encounter in the foundry, the T-800 slams on the SWAT van's brakes and the helicopter slams into it, crushing the choppers front. A second later it is in reasonably good shape.
Continuity mistake: Throughout the aqueduct chase, the crane on the back of the semi goes from swinging back and forth in an upright position to being bolted down about four times.