Stupidity: The Analyst wishes to hide the true identity of Neo from anyone inside the Matrix, so his appearance is altered. But in this new Matrix Neo is also named Thomas Anderson, his name from before he was pulled from the Matrix originally, and he is a famous game developer that created a video game series called "The Matrix." It is frankly astounding that anyone actively looking for Thomas Anderson would not immediately see through this ruse and instead would be fooled by balding hair.
Stupidity: When the duke approaches the wall at the end, Snake dives on him and briefly knocks him out. Snake could have easily grabbed his gun back and left the duke unarmed (or even just killed the duke there and then), but just gets up and runs, leaving it with him.
Stupidity: Throughout the movie, and especially up on the top of the apartment building before they get rescued at the beginning of the movie, Gerry counts 12 seconds to check if someone has been infected. Just to mention this apartment example, he gets blood on his face and spends more than 12 seconds getting up and to the edge of the roof, plenty of time to become "Zeke." He then counts 12 seconds, as if they would actually matter to his infection.
Stupidity: After making love, Selina notices Batman's scars. She surely was caught in the moment, but, it's something she really was bound to notice sooner. (00:53:10)
Suggested correction: She notices the scars on his back first, which are the worst of those on his body, this may well be the first time she sees his back.
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: 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: Since we get frequent POV shots from their eyes, we see exactly what the creatures hunting Venom see. Even when the Codex disappears from their view, they can see distinctly Venom's shape, and they have no problem using their appendages and brute force against any and every creature. There are moments in the movie (such as the scene in Vegas) when the Xenophage just stops for no reason; even if the big blinking thing is gone, you can still see the shape it was attached to.
Stupidity: Cobb convinces Fischer to enter a dream saying it's Browning's dream. A couple of scenes later he says it's Eames' dream, in front of Fischer, who doesn't know Eames was impersonating Browning. (00:51:35)
Suggested correction: Firstly, the Browning that the team "catches" is not Eames, it is a projection of Fischer's subconscious. Eames was only impersonating Browning in the first level. Secondly, Cobb doesn't say they are going into Browning's dream, he says they should put him under and do to him what the kidnappers were planning to do to Fischer. That is, use Fischer as the subject of the next dream level. Fischer knows that Eames is the dreamer on the third level, he even jokingly asks why Eames couldn't dream of a beach. But he thinks that Eames is part of Mr. Charles' security team. He believes that Browning is to be the subject on the last level when in fact, Fischer is the subject on each level. Because of how effective the Mr. Charles gambit was, Fischer is unaware that the team has been fighting his subconscious all along.
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: 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: 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.