Plot hole: In the scene where Ashley Judd runs away from her attacker and falls into her aquarium he has moved to the bottom of the stairs - there is no way he would have been able to move that full fish tank. It looked to be about a 30 gallon tank - it would weigh about 400 pounds with the stand and even if he slid it with some superhuman strength, glass tanks are notorious for shattering when you move them full. Plus it would've made enough noise to wake the dead - no way she wouldn't have heard it.
Plot hole: At the start when the guys are infiltrating that building they parachute down to the roof. They are dressed in black so they can't be seen, but their parachutes are white. (00:02:50)
Plot hole: Kazam is supposed to be a math genius, something that the plot hinges on, but he makes several mistakes when calculating the number of prime factors to find out whether a room is trapped or not. He says that 462 has three prime factors, when it has four, that 206 has four when it only has two and that 563 has two and 911 has three when both are actually prime numbers.
Plot hole: During the Congressional hearing, it is suggested that the alien signal could have been faked from a satellite - as Ellie only has her own experience to go on, it leaves her believing what happened, but still with an element of doubt. However, as a professional astronomer, Ellie would have immediately dismissed this since a simple parallax (triangulation) would have confirmed that source was at the distance of Vega - a distance far too great for any rocket to reach. (This is mentioned in the book). In fact, this is mentioned early in the film, when the employees in New Mexico calculate the source of the signal while it is transmitting prime numbers.
Plot hole: When they are trying to find a way to stop the lava from going in to the museum, Tommy Lee Jones has an idea to push a bus up against the museum to divert the lava. The plan works but the lava does not melt the bus like it melted Tommy Lee Jones' car or the fire truck. Even though the bus melts later in the movie, it doesn't melt it instantly like it did with the fire truck.
Plot hole: Jennifer Ehle gets a note from her husband, who is a prisoner in the men's camp a few miles away, saying, 'We're escaping on Sunday night. See you in Sydney.' So, even though this note is going to be passed via several people, any of whom might betray him, not only does he explicitly say he plans to escape, but even when he's going to do it. No wonder he gets caught.
Plot hole: Interesting to note...in the opening scene where Pete is talking to Jack, Pete says that the boiler pressure needs to be dumped every night or it'll blow because the safety valve has been rusted shut for the last twenty years. Then he continues on to say that last year's caretaker, Grady, killed himself, and he was alone at the hotel. So...why didn't the boiler explode last winter? (00:02:20 - 00:05:55)
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.
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: 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)
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.