During interrogation Kuze removes half of Major's robotic face, and her hair falls over the exposed left eyeball. He then replaces the half-face without first brushing this hair out of the way, yet in the next shot she looks perfectly normal.
After Batou meets Major on the boat, they sail off towards the bridge but, when the camera switches to a wide shot, there is no wake behind the boat and it's not moving.
When Cutter confronts Aramaki in his office from across the desk, Cutter's hands don't match. When the camera is behind Cutter, his hands are balled up and he is leaning on the desk on his knuckles. When the camera is behind Aramaki, Cutter's hands are flat and he is leaning on the desk with his fingers straight.
When Aramaki's car is shot, the bullet holes are in a tight cluster in the door but, in the next shot they are more evenly spread out.
When Major visits who she suspects is her Mother, and they sit down at the table for tea; with each character's point of view to the other switch, the tea pot handle is up (from Major's view) but then down from her reverse (Mother's view) shot: and the kettle that boils the water whistles its ready - yet has now whistle attachment to its spout.
In the car and suitcase shooting scene, Aramaki somehow manages to fire 8 shots out of a 6-shot revolver without reloading. That his revolver only holds the (typical) number of 6 cartridges is clearly visible in a close-up in previous scene.
When Major meets Motoko's mother for the first time, she puts the kettle on the stove to make tea and it whistles. However, the kettle on the stove is not the whistling kind, which has a distinctive spout.
About 24 minutes, Dr Dahlin is analyzing a destroyed robot geisha. She says "This will take days". Next, she immediately describes in precision what occurred.
When Major shoots the geisha robot in the face, the robot's face is open, revealing its inner workings. The face then closes and, when next seen, the impact patterns from the bullets smoothly cross the seams of the closed face which they would not do if the face were shot when open.
At about the 42:55 mark, Batou and Major are in his car when they get news of another Hanka scientist's' death. Batou spins the car to the right and performs a 180° turn, then drives out of frame toward the camera view. He could have just turned left in the first place.
Batou asks Major to feed the dogs for him, as he doesn't want to scare them with his new cyborg eyes - but dogs would only care that he still smells the same.