Plot hole: Al Simmons' reasoning for wanting to quit A-6 is because he learns his rocket attack in his assassination mission in the beginning of the film yielded civilian casualties. This makes no sense, as he blatantly gunned down several innocent men in the air control tower just moments before.
Plot hole: They show the two men trapped inside a ring of fires that they have built, (and must constantly maintain to keep the bear at bay), as the sun is setting. And, somehow, when the sun rises, they have created enough rope, (just from grass and bark, I guess), to tie a huge boulder from way up in a tree - all wrapped with ropes and spikes, and have somehow deployed that, and stationed a bunch of other sharpened spears in various places, over hundreds of yards.
Plot hole: Kahn's death makes no sense. In the film, Rayden explains that the dragon tattoos flee one's body upon the person dying. And yet, Kahn is still alive and not even close to death when his tattoo flees. (Which is what kills him, since it rips him open when it flees.) It's like they couldn't figure out how to kill him in the script, so he's just spontaneously is killed by his tattoo, even though it violates the rules the film set up.
Plot hole: Jordan doesn't complete the course in under 12 minutes, yet master chief states she gets the standard 30 second deduction. But that still doesn't put her under the time limit.
Plot hole: Regis could have saved himself a lot of time and solved the case much quicker if he had just verified the entries in Carla Town's day planner with the businesses listed. A few phone calls would have told him the entries were forgeries without going to the technician for help.