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: It makes no sense that Martin would be getting the invitation to the reunion mailed to his office (or to anywhere else.) He's had zero contact with the alumni committee, and they're not going to hire a private detective to find him. He also doesn't have contact with anyone else from his hometown who might have forwarded it; his father's dead, and his mother's not in her right mind. There's no explanation for why it would have ended up there except for needing to set the plot in motion.
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: When Luther places the envelope on the table during the White House tour, he is not wearing gloves, thereby leaving his fingerprints behind.
Plot hole: In the waning seconds of the championship game, the Huskies are down by 2 and UMass has the ball. Not only do the Huskies not intentionally foul to stop the clock, but UMass attempts to run a play and set up a basket when they simply could have dribbled out the clock and won the game. Both these strategies go against what any basketball team would do in this situation, especially in a championship game.
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.
Plot hole: Marcus told Melena he lived in New Mexico with his parents until he was 5 years old: "My dad died in a car accident when I was five... and my mom got caught smuggling people into the country, so she got 10 years [in prison]." Even though Marcus did not know at the time the real reason his mother was in prison, the murder must have occurred in New Mexico, so it doesn't make sense that she would be serving time in a New York prison. (00:33:20 - 00:34:21)