Stupidity: When the Keymaker is closing the door to the room that leads to the Source, he stands in the doorway resulting in the multiple Agent Smiths gunning him down. He could have easily closed the door without standing in the doorway and consequently would have lived.
Suggested correction: Who says the door was bullet proof and the Keymaker couldn't have been shot through the door?
The point of the stupidity is that he shouldn't have been in the doorway at all, even if the door wasn't bulletproof, there was no need for him to even stand behind the closed door. He could have pushed the door closed from the side.
It seems to be a heavy door, he simply couldn't close it with just his arm, thus he had to move his body forwards in order to close it. In that brief moment he got shot before the door closed. He could have for example kicked the door shut but he simply didn't think of that at that moment, also not knowing the Smiths were about to fire a volley of bullets at them.
Stupidity: Oldboy finds the right Blue Dragon restaurant that the prison uses. But him running after the delivery boy doesn't make sense. How does he know the delivery boy is going to the prison? He knows it's the right takeaway, but that's all he knows. So, would he have a moped, bicycle, or car ready to use surely? The takeaway is a long way from the prison (as he says himself in narration), so he wouldn't just wait around for a moped delivery to run after, especially as a good chance he wouldn't be able to keep up.
Stupidity: The prison where Magneto is held should have had a contingency plan just in case of escape, like machine guns outside the cell, or tranquilizer darts, or gas.
Suggested correction: What good would machine guns and tranquilizer darts be against a man who can literally control and manipulate metal? As for gas, the area outside the cell is so large that any gas would quickly dissipate before it could be effective.
Stupidity: If the doctor was able to choose the people to go on the helicopter, why didn't she make up a reason to put the president's son on the helicopter for his safety? She could have said he was sick. (01:14:40)
Suggested correction: He is shown to be a caring person. There is no way he would take the place of a sick woman or child just to save his own neck.
That correction is illogical though. By not getting on the helicopter he puts everyone else at way more risk. It would have made getting the rest of the people left behind out of danger much easier as they wouldn't have been hunted down by the people who were chasing the president's son. By not getting on that helicopter he could have gotten everyone killed.
Stupidity: Why would Stanley say the shoes fell out of the sky? It happened under a bridge. Any normal person would instantly realise someone threw them off the bridge.
Suggested correction: It's an idiom/expression. When something turns up out of nowhere, we say "it came/fell from the sky." In fact, Mr. Sir says this to Stanley when he finds Stanley with his empty bag of sunflower seeds, "Where did this come from? Did it fall from the sky?" Obviously a sarcastic way of saying, "it didn't get there by itself, someone put it there." So the shoes obviously fell from the bridge and Stanley knows this because Zero refers to the bridge later in the movie.
Stupidity: If there was a live camera feed right where the eggs were, one wonders how everyone missed the 'small' fact that they hatched. That of course combined with the fact that going for no reason in the nest of the creatures that nearly killed another crewmember is suicidal, and Bob goes with no weapons and with one small plastic fruit crate to fetch eggs that are bigger than an ostrich's. (00:55:25)
Stupidity: When Governor Swann is trying to encourage his daughter while she's locked within the ship's chambers trying to escape, she climbs down to a boat. Nobody in the Navy would have left a boat there, neither would Jack (and why would he, especially without anyone noticing?). The boat just mysteriously appears to help her escape.
Stupidity: During the film's climax where Santa and his reindeer successfully ascend over Manhattan, the sleigh's rocket engine falls off and apparently is no longer needed. Isn't it rather risky (and foolish) to assume (or hope) that the other cities on his flight path have enough "belief power" to sustain him aloft for the rest of his journey?