During the fight when Jack and Neytiri rescued their children, they kill 4 soldiers from a party of 6. Yet at the extraction scene, all 6 soldiers are present.
In the first film, Dr. Grace Augustine tell Parker Selfridge about the Na'vi's ability to upload and download memories, which Parker Selfridge responds, "What the hell have you people been smoking out there?", meaning such technology did not exist then. In this film, they watch Quaritch's log and such technology existed when he was alive.
At around 2:17 spider is shown running off the bridge down to the deck. While on the bridge and running he is not wearing his mask/breather but has it on when he reaches the deck.
When Lo'ak is being chased by the shark-like creature through the corals, there is a moment, just before he begins to convulse, where the white feathery creatures attached to the coral next to Lo'ak's head seem stiff and plasticky, as if they forgot to animate them. In the next moment, the same creatures are swaying softly in the current as expected.
Spider talks about the moon pool of the antagonist's ship (a moon pool is an opening in the bottom of the hull, giving access to the water below). The Italian version translates this as a meaningless "pool shaped like the moon".
The main characters leave their home village so that the bad guys coming after them will no longer target the village. But the bad guys don't know any of this, and no effort is made to tell them. This defeats the stated purpose of leaving.