Continuity mistake: After John crashes the truck into the silver car, the empty emergency vehicles approach from behind. At the right, a red sedan is shown from the rear with a broken tail light and mangled bumper. A few shots later, the crane comes around a corner and hits this red car, but before the actual collision, the tail light and bumper of the car are fine. (00:31:55)
Continuity mistake: When John and Kate are in the bunker and they are talking about why they are there, we see John look down at the timer. It reads one minute 16 seconds. When Montana Civil Defense is talking over the radio, he deactivates it at 7 seconds. It should have read 27 seconds; there had been no breaks in the scene. (00:38:50)
Continuity mistake: When John and the vet arrive at the mountain in their Cessna, the sun casts a shadow straight under the plane. The very moment they walk through the door into the hangar integrated in this mountain (which in the film is immediately after they landed), their shadows are in front of them indicating a low sun. (01:30:45)
Continuity mistake: When the Terminator puts the tyre wrench in the doors of the van he bends the wrench. But later in the desert it's bent differently. (00:25:15 - 00:41:40)
Continuity mistake: The driver side rear view mirror is broken on the police car as it chases the tundra truck onto a front yard, but after leaving the yard the mirror is back intact. (00:34:55)
Continuity mistake: During the big chase scene (a little after the Terminator collided with the fire truck), the crane crashes through another glass store front. When it emerges and turns, the hook is tied to the front of the crane, just as it was when the T-X first got it. (00:36:30)
Continuity mistake: When the T-800 first drives the truck into the Vet clinic, the truck has crashed into the building, so that the doors are inside the clinic. Yet in the very next shot when he gets out, the truck has moved back so that the doors can open cleanly, without the T-800 backing the truck up. Then when John escapes the cage and he runs into the T-800, you can see the truck inside the clinic. It is now more than halfway inside the building. (00:24:15)
Continuity mistake: When the TX's crane is pulling away after destroying the building facade, it is seen from the high angle that the top of the cab is clean. When the crane is shown again the cab roof is covered in cables and other debris. Also note it remains this way until catching up with Connor in the Tundra truck and then the crane is clean like it was run through a car wash.
Continuity mistake: When the Terminator is hitting the T-X with the fire extinguisher, she puts her fist up and punctures it so the Terminator chucks it down on the floor. We see it on the floor again, but when the Terminator is running towards the T-X you see where the extinguisher was but now it has vanished. (01:18:55)
Continuity mistake: When Katherine Brewster is initially saved by the Terminator from the TX and thrown in the back of the truck, her knees are wet, then drier and drier but then wet again showing the sequence we see was shot at different times. (00:25:30)
Continuity mistake: During the shooting scene at the cemetery, note one of the stones (rectangular from the left) behind T-101 when he comes out carrying a coffin. You can see it has 5 holes - 3 left, 2 upper right side. However, a few seconds later, it has 6 holes, but their position has completely changed, 3 upper side, 3 right side. (00:55:25)
Continuity mistake: When the Terminator is at the AM/PM, he is filling a small basket with various food items. One item in particular was a large bag of chips. The contents in the basket change from shot to shot, most noticeably the chips disappear completely. (00:42:35)
Continuity mistake: When smashing the truck in the hangar, the T-850 hits it and it falls down so that the bumper is on the floor. When it shows the T-850 from John's POV, the truck is back up on its wheels, although the wheels are still damaged. (01:29:05)
Continuity mistake: When Kate takes a gun out of the coffin at the cemetery, you can see she puts her finger on the trigger. In the next shot, her finger is back around the handle and not around the trigger.
Continuity mistake: The amber parking light lenses on the hearse are mismatched and change several times thoughout the hearse scenes (note the Cadillac crest on the left side lens).
Continuity mistake: When the T-X steals the car in the beginning, she's weaving in and out of traffic and from her view we see that she is coming up to a truck in the right lane. The view changes to view from outside the car and she's turning into the right lane and driving straight ahead. The truck is gone. (00:07:50)
Continuity mistake: When the Terminator jumps onto the roof of the truck that John is driving, the damage he causes changes when we see the truck driving off into the distance. (00:37:30)
Continuity mistake: During the crane chase the amount of damage to the van changes drastically throughout the chase. (00:33:35 - 00:35:00)
Continuity mistake: When John, Kate and Arnie are at the cemetery getting the weapons from Sarah's casket, Kate pulls a handgun on Arnie. He looks up and is facing his right with his legs turned in that direction. They go back to Kate and then back to Arnie. Now he is turned to the left. (00:51:05)
Continuity mistake: In the crane chase scene, there is a point where the last remaining ambulance collides with the back of the Toyota. You see the ambulance back off and the right headlight is smashed and the housing is dangling. The headlights are also off. The scene cuts to the rear-view mirror of the Toyota. You briefly see the same ambulance with its lights on and both headlights are intact. Shortly thereafter, they cut to a behind-the-back shot of Arnold as the same ambulance starts to flip. The tail lights are on. It wouldn't be brake lights since there is no driver and the Terminatrix certainly wouldn't remotely apply the brakes.
Answer: He was originally in talks - and by some reports, did appear on set for some period of time. While factual answers are in short supply (for obvious reasons), there appears to be a connection to his drug-use habits. For instance, he was checked into a hospital (LA Cedars Sinai) for what friends feared was a drug overdose in April 2001, and has been in and out of rehab over the years. Chances are the production company was unable or unwilling to get completion insurance.
Rooster of Doom