In the scene where Jake wakes up from his link and Grace asks him, "Is the avatar safe?" and he replies, "Yeah Doc, and you are not gonna believe where I am," her hand is on top of his shoulder. But as the camera angle changes back and forth her hand switches to the side of his upper arm and back to the shoulder without time to have made the move.
In the scene where Jake first meets Neytiri and is trying to thank her, he grabs her arm, however, the sound effect for grabbing her arm isn't in sync, as you can hear it a couple seconds before he does grab her arm.
During one of Jake's video logs, Grace can be seen working on an experiment in the background. In the process, she draws up some liquid in an Eppendorf pipette. However, in the process of transferring the liquid to its intended vessel, she inverts the pipette, which would severely damage it.
During the shot where Quaritch says to Jake "That's called taking an initiative son", Jake's hands are rested up on the hologram table. In the next shot where Quaritch says "I wish I had ten more like you", Jake's hands are down at his sides.
In the scene where Parker is shown playing golf on the indoor golf course in RDA, the first time he hits the ball, there are two other balls lying on the course side by side. In the next shot, two are distant from each other and in the shot after that, they are in their original position.
Jake is reviewing the structure of the home tree with Quaritch and Selfridge around the rotating 3-D map. When Jake makes a comment about the Na'vi studying him, his watch reads 2:19. Selfridge makes a comment about how the tree is sitting right over the richest Unobtanium deposit. When the camera cuts back to Jake his watch now displays 2:53.
In the colonel's robot there is a rear-view mirror. When we see the robot from the outside, it is very close to his head. But when we see shots from inside the robot, there is plenty of room around his head and we don't see the mirror.
When Jake is recording his first video log entry, he moves the recording camera around a little to get a better view of his face, and is looking directly at a screen to his right to see if he's centered his face correctly. In the very next shot, he is staring straight forward at the camera.
When connecting with the Mountain Banshee for the first time, Jake's hair switches from being over his right shoulder to being over his left between shots. (His hands are on the Banshee the whole time so he had no chance to change it.)
When Seze first comes out of the tree, if the viewer watches carefully, he/she can see Neytiri's ponytail being flung over her left shoulder, indicating that it would be hanging down her front, but in the next shot it was hanging down her back.
When Jake follows Neytiri to thank her after the first time they meet, Neytiri is carrying her bow and an arrow in her right hand. After knocking him down, and after Jake tries to thank her, for a few seconds on screen the arrow disappears from her hand. A Few moments later, the missing arrow returns to being carried by Neytiri in the same hand that has been holding her bow all along.
When Parker Selfridge wants to explain the situation (the 'Blue Monkeys') to Jake and asks someone to operate the hologram showing the layout of the landscape he says stop at sector '12' (Hometree), but when the scene cuts to a closeup of Jake the yellow hologram readout clearly reads 'Sector 128'.
As the dragon gunship takes off to join the formation for the finale battle it can be seen with a total of eight white missiles on eight weapon pylons; four on either side. Later on it only has four missiles on only four weapon pylons; two on either side.
In the scene right after the destruction of home-tree, when the people in the link room cancel the link in progress and Jake Sullys Avatar body goes limp, his Avatar is lying on his back with his head facing toward the left side of his body. Later, when the whole crew is able to escape the jail cell and move the mountain side base, Jake links back up with his Avatar and his head is facing straight up.
As Jake is pulling his legs into the linking machine for the very first time, we see Grace's hands near his legs as if moving to help him. However in the next shot she is few feet away and then moves to help lift Jake's paralyzed legs.
A large mining machine, a bucket wheel excavator [BWE], is seen during the shuttle landing sequence. It is shown operating incorrectly, with the descending part of the wheel against the rock. A BWE operates with the ascending part of the wheel against the rock, so the spoil can fall into the buckets.
Any robot in Avatar is always standing up and will remain static until its operator gives it a movement command. However, when Neytiri kills colonel Miles Quaritch his robot falls to the ground as if it had been killed.
In the scene where Jake is looking at the photographs of the Na'vi on the refrigerator, the photographs themselves are 3D. This is an invention which exists since 1940 and is called lenticular printing. We can only assume that, like much of the technology in the movie, the quality of those prints has advanced by 2154.
The helicopter-like aircraft makes the sound of an ordinary helicopter - this is not correct: high-speed framed propellers produce an entirely different, quite unique buzz-like, smoother noise at a higher pitch. However, we know that they are operating in an atmosphere which is entirely different to Earth's (humans have to wear masks) and lifting an aircraft in gravity which is different to Earth's (it is stated that the humans have to work out in the low gravity), so we can't really make any comment on what these propellers should sound like.
When Selfridge lectures Grace in his office about the corporation's purpose on Pandora (mining 'unobtainium') he closes with the Spanish expression "Comprendo?". This is grammatically incorrect as it would mean "Do I understand?". Addressing Grace, he should have said "Comprende?" (Do you understand?). However, his language mistake shows his lack of appreciation for other cultures.
The first part of the credits are shown over panoramic views of Pandora. Most of these shots are recycled from the movie, and reversed left to right to make it a bit less obvious. One in particular was taken from Jake's ikran first flight sequence, but with Jake and the ikran removed. But you can still the ikran's shadow pass over the rocks.
In the scene where Jake lands on Pandora for the first time, when all other personnel have gotten off the transport ship it is revealed that Jake is paraplegic. When he gets up from his seat into his wheelchair, after lifting his legs from the seat with his arms and putting them in place on the wheelchair, you can see him moving his left leg a bit backwards (without touching it).
Jake walks up to the Tree of Souls to pray to Eywa with his ponytail down his back normally. Jake kneels before the tree, with the ponytail in the same spot. Jake reaches down for something, the shot changes, and the pony tail appears in his hand. This was likely done to match Sam Worthington's performance as he was not holding it as he approached the tree, and it would look unnatural for him to do so, being at odds with the motion capture data.
In the first battle sequence, Jake is seen shooting his weapon upwards, towards a helicopter. However, in the next sequence, the helicopter is shown being hit, but the bullets are coming down, opposite from the direction Jake shot them.
In the nightclub scene on Earth when Jake is thrown out into the street, you can see his legs move and stiffen into a bent position (which are supposedly paralyzed) in anticipation of landing on the ground.
The goof items below may give away important plot points.
Jake Sully pulls a blanket over Grace Augustine in the scene where they are flying north in the mobile link-up trailer after Grace is shot and leaves it folded at the top. The next shots alternate showing the blanket flat with no folds and the blanket with folds.
Though it would seem Norm is standing next to his Avatar near the end of the movie (which would be physically impossible) we see multiple avatars with trousers and guns in the background. These are likely the other avatars we saw at the beginning of the movie.
In the scene where the Na'vi are attempting to move Grace from her human body to her Avatar body, after she has died and one of the Na'vi moves to check for life in her Avatar, you can see her eyes twitch even though she is supposed to be dead.