Minor Plot hole: When Jake Sully's avatar was lost in the jungle; it is far-fetched to believe that the humans on Pandora could not spot him via some sort of GPS technology that could locate where Jake's home signal is going. Furthermore, since Avatars are one of the biggest investments of the company, they would probably have implanted a device in their flesh to know exactly where they would be at all times.
Major Plot hole: Trudy Chacon refuses to attack Home Tree and decides to leave the squadron. She then does not seem to have been punished for disobeying a direct order from Colonel Quaritch and is able to save Jake Sully from his cell.
Major Plot hole: There is no reason for Colonel Quaritch to go outside and shoot at the hijacked helicopter with his handgun while they have automated anti-aircraft weapons in their base (shown at the beginning of the movie). Jake/Trudy's escape attempt was also spotted by the command center before they even took off and it would have been really easy for them to take it down.
Major Plot hole: The spaceship that was supposed to bomb the Tree of Souls could have simply bombed them from a higher altitude where the flying creatures could not breath. There was no reason for it to fly that low. Yes the action sequence was great - but James Cameron needs to try to get sexually aroused with logistical screenplays and not just 3d cameras.
Plot contrivance: Warfare technology in 2149 is only slightly more advanced than Warfare Technology in 2010. If technology really followed it's current exponential trend; human warfare technology would be far more advanced and would have no problem dealing with Pandora's animals. We're talking about a future in which not only can we combine our DNA with freaking aliens from other planets, but we can control organic beings (the Avatars) from afar. So how is it that the humans have achieved something that's impossible today, but yet won't use today's possible technology in the future. There is a lot of talk that our military in the near future may soon begin to downsize as we increase our use of technology and unmanned vehicles and aircraft, just like every other industry in America.
Unaddressed Issue: Colonel Quaritch mentions that gravity is less powerful on Pandora. But just like your dad telling you for the first time that sex exists when you are a teenager, this concept is never brought up again.
Unaddressed Issue: Almost all the aircraft in the movie have rotary style systems, like a helicopter, which explains their vertical take off and hovering abilities. however, the spaceship the humans use to bomb the Navii in the final scene has no rotary blade system at all. It was also the same space craft that ferries people to and from Pandora across space. But by the way it is fling in the last scene (without rotary systems) we must assume it has some form of anti-gravity technology. But if that is true, then why does it need wings? One might think the only critera here was the coolness factor.
Unaddressed Issue: In the scene where both grace dies trying to switch bodies and Jake does so, it is never explained how the Na'vi know how to do this. This ceremony has no other use besides transferring a soul into a "soulless" empty body. Unless they go all search for Spock on each other every once in a while, how do they know this is possible? (by Cheeseofborg)
Unaddressed Issue: We all understand why some people (especially the main characters) would be upset with the human's treatment of the Navii people. But I cannot understand why some humans would fight against their own species and end up staying with the Navii. Obviously, Jake has the opportunity to transfer his consciousness into his Navii body, which allows him to breathe the Pandora air. But many of the other humans who side with the Navii don't have cloned Navii bodies. They might agree that the treatment of the Navii by the humans was immoral, but why stay on Pandora? Eventually they you will run out of air, and it's not like the company will send them some cloned Navii bodies (with wings!) via galactic FedEx.