
Stupidity: After Noah shoots the Humanity Bureau vehicle following them, they continue down the road and stop at an old abandoned building that still has some sort of running water in it. Lucas has to go to the bathroom so his mother just lets him wander off by himself to find a restroom. She doesn't go with him or make sure he's fine. And this is in an area where they know that most of the residents are hostile, and they are being chased by the Humanity Bureau. Noah even calls her out on the stupidity of her letting Lucas go by himself and she claims it's because he needed to do number 2 and that Lucas insisted and he's not a little kid any more... Which doesn't excuse the stupidity of the action of letting an 11 year old go by himself to find a bathroom in such a situation. And ultimately it does lead to him getting found by Agent Westinghouse. (01:08:30)

Stupidity: I won't begrudge Father Lamont for instinctively grabbing for the first thing in reach to try to smother the box on fire (even if it is a pair of wooden crutches), but you'd think at some point he'd notice that he's just spreading the fire and making it much, much worse, but he keeps at it until the doctor finally returns with the extinguisher.

Stupidity: When the plane begins crashing, Kayla tells Claire that she is sitting in an ejector seat. She also mentions that there are no parachutes because she "wasn't expecting company." If Kayla was expecting to be alone in a crash scenario, what use would installing the ejector seat in one of the passenger seats have been? She would have to move from the pilot seat to the passenger seat while the plan is crashing. Surely it would've been easier to install the ejector seat in the pilot seat.

Stupidity: Despite the fact that the villains know exactly where Brogan is for the better part of the movie thanks to a tracer, and that they display constantly that they are able and willing to hit with bold military operations even to the point of hitting an urban area overruling law enforcement (apparently Clay has authority to do that too), Brogan is able to get undisturbed back in the US through his friend's plane. Considering he was officially marked as a rogue agent and killed 8 DIA operatives, it's hard to see how Baron's plane could ever land on American soil after a long intercontinental flight.

Stupidity: Dr. Emma Collins and Shaw were in the water with Sally the Great White Shark. Emma put her right hand over Sally's nose and pushed her back. Sally swam forward and Emma pointed her index finger at Sally's nose then pushed her back again. Emma told Shaw, "If you stay calm and redirect" and "Don't try this at home" before Sally pushed Emma with her nose on Emma's stomach and rammed her into an underwater object. Emma was the instigator, goading a Great White Shark. Emma could have been killed. (00:05:10)

Stupidity: Charlie set her mom's blouse sleeves on fire and mom/Vicky just stood in the same spot, holding her arms (burning sleeves) out in front of her until Andy came and smothered the flames with a blanket. Even children know to "drop and roll" or put fire out by smothering it. (00:22:56)

Stupidity: Dr. Cocteau's choice to unleash an enhanced Simon Phoenix without any way to restrain him is incredibly reckless and stupid. Even if Simon were to kill Eager Friendly, in the best case situation, you'd still have a madman with total computer access, martial arts knowledge, etc., that you would have no way to rein in. Sure, he can't kill Dr. Cocteau, but what would stop him from say, holding the city hostage or something? Why not add in a kill code or something to keep him in check?
Suggested correction: Who says he didn't? Cocteau has put in mental conditioning compelling Phoenix to kill Edgar Friendly and make him unable to kill Cocteau. Who says he hasn't put in something that makes him kill himself after the deed is done? Or perhaps paralyze him so he can be put back on ice. It's just that Cocteau didn't count on the fact that his henchmen could kill him. He doesn't care about how dangerous he is, not until he has done the deed.
Dr. Cocteau is a narcissistic egomaniac type that would see himself as a king or a god, even. And Simon is making him very angry. He even tells Simon, "you're beginning to be more trouble than you're worth..." Someone with an ego like Cocteau wouldn't stand for Simon's antics for very long. And would happily enjoy putting Simon back in his place by shocking, paralyzing, etc.
But he first needs him to kill Friendly. Until he does that, he'll let him play. He still sees no danger to himself.

Stupidity: Right before the movie's final battle, Sub-Zero taunts Cole with his wife's necklace and makes him chase him into a portal. Sonya was right next to Cole, and she did not come along with him. They had previously planned to take on Sub-Zero together, but apparently she just left him to chase Sub-Zero alone to an unknown location.

Stupidity: When Jody traps Michael in his room, he does so by sticking a screwdriver between the the door and the jamb. This likely wouldn't accomplish much regardless, but it especially wouldn't work in this situation because the door opens into the room, so Michael could simply open the door and the screwdriver would fall on the ground.

Stupidity: In the Anubis universe, immediately around the time Lawless says, "Something's wrong," if you look closely, by Lawless, you see the two police officers behind Jet Li walk away to leave Lawless completely unprotected from behind. I understand it's a parallel universe, but that's some really bad police work to leave a prisoner wide open like they do.

Stupidity: While the train cars are still derailing in front of them, the kids stay on the porch and actually start running toward the oncoming train. Next, they turn around and run in the opposite direction, while staying the same distance away from the train tracks and flying cars/debris. When they run out of the porch to stay parallel to the train, they again turn around and run to the middle of the porch and look like they are jumping around together, clueless where to run to next - running in either direction parallel to the train was not getting them away from derailment. Then they disperse in various directions but stay off the porch. (00:17:24)

Stupidity: Jimmy and his friends aren't allowed by their parents to go to the opening of Retroland because it is a school night. What kind of amusement has its grand opening on a school night? It would make more sense commercially to open on a Friday or Saturday night.