Revealing mistake: When the T-800 is reloading his shotgun in the alley with John, he reaches into his pocket, presumably to grab shells for the shotgun. In the shot with him and John in frame, his hand comes out of his pocket empty, but we hear him load another shell into the gun in the next shot.
Continuity mistake: When the helicopter smashes into the back of the police van the front gets completely smashed in and crumples. Next shot is from the side - the helicopter falls to the ground and the front is intact, then smashes to pieces on impact.
Continuity mistake: When Sarah uses her shotgun to shoot the T-1000 in the eye, the first camera angle reveals that the shot has disfigured his head forcing the tissue around the eye to be pushed outwards as a result. In the next shot, when we can see Sarah through the hole as it 'heals', we can see that the head is already in its regular shape as the hole fills.
Continuity mistake: As the liquid nitrogen tanker crashes into the SWAT truck, the semi's right headlight is destroyed, but a second later it's back in position, and no damage to the nose of the semi at all.
Visible crew/equipment: As Sarah starts to slide to a stop as she sees the Terminator, you can see the shadow of the camera on her left shoulder and arm.
Revealing mistake: When the T-1000 goes to kill the guard in the mental hospital, from the angle looking at the T-1000 the seam where the prosthetic matches into the guard's skin is visible.
Continuity mistake: After John gets off the bike, he looks at the Terminator's back and sees the holes in the jacket. John puts his finger in one hole, but when the view changes the finger is in another hole.
Visible crew/equipment: In the shot of John riding under the bridge just seconds before the roof is ripped off the truck, the shadow of the camera is moving along the floor by John's bike. (00:35:15)
Audio problem: In the scene where John is running away from the T-1000 in the corridor of the mall, one of the curators shouts out "Hey!" The Terminator appears in scene so John runs back the other way passing the same curator he ran past before who then shouts out "Hey!" at him again. The curator's mouth never moves during both of his lines. (00:31:30 - 00:31:53)
Continuity mistake: When Terminator shoots at the police from the Cyberdine window, from the angles in front he is in the middle of two window frames, yet from the angle shot from behind he is inches away from the left frame.
Continuity mistake: At Pescadero, after Terminator pushes a female guard away, John runs to Sarah and asks if she's okay. Her body is positioned pointing in an 8 o'clock direction first, and in the following shot in an 11 o'clock.
Continuity mistake: At Pescadero, when the female guard breaks Terminator's glasses, from the angle behind the left lens is pointing upwards, yet from the front it's downwards and the damage is greater.
Continuity mistake: When Sarah sees the Terminator coming out of the elevator and crawls backwards panicking, there's a thick line painted on the floor. When the angle changes and shows her standing up and running, the line is gone.
Continuity mistake: When Sarah is about to jam the syringe in the plastic jug, watch its label and notice it turns around between frames.
Continuity mistake: At the hospital, when Sarah is dreaming of Kyle and rests her hair on his left shoulder, her hair swaps from messy to brushed between shots.
Continuity mistake: When the T-1000 is on the police car's trunk, the hole he produces on the windshield increases and decreases in size between shots. (01:02:40)
Continuity mistake: Sarah takes the chip out of the Terminator's skull and places it by the edge of a table. In the next angle, it is several centimeters away from the edge.
Continuity mistake: In the police car after escaping from the T-1000, John's hair is moving to the left because of the wind. When the angle changes to a POV from the driver's seat, right when he says "I had to get you out of the place", his hair is moving wildly to the right, then a frame later, from a new angle, it's back to the previous mild movement to the opposite side.
Continuity mistake: When the fat cop is killed, blood on his nape and collar appears and disappears between shots.
Continuity mistake: When escaping out of the parking lot, John drives past the same blue pick-up truck twice.
Answer: In addition, another deleted scene shows that the T-1000 was damaged by being frozen and thawed and was having difficulty maintaining form. He wanted to be sure he wouldn't mess it up.
LorgSkyegon
What's especially odd about the scene is that both examples we gave to help answer this question were actually deleted from the original release. When I first saw this movie in the theater when it was released I had the exact same question, it wasn't until I saw the Special Edition with the deleted scenes reinserted that it made sense.
BaconIsMyBFF