Stupidity: When Anna, Velkan and the villagers successfully trap the gray werewolf in a huge cage, the villagers start firing on it. Anna says they need to use Velkan's gun because it has silver bullets in it. Since everybody knew they were fighting a werewolf, all of them should have had silver bullets for their guns.
Suggested correction: They lived in a remote mountain village and obviously did not have a very luxurious life. So they simply did not have enough silver to make bullets for everyone. They could only afford one gun with silver bullets. But they loaded their guns with normal bullets because that at least made them feel a bit more secure compared to going against a werewolf bare-handed, even though normal bullets were actually useless.
This entire correction is full of nothing but conjecture.
That a remote mountain village in 19th-century Transylvania did not have enough silver to fill every gun with silver bullets offers a plausible explanation of why they did not use silver bullets in every gun. You cannot fill a gun with something you do not have.
Stupidity: The Engineer and Fireman of the Polar Express train crew should have known better than to not bend back the the metallic prongs of the cotter pin, which would have prevented the cotter pin from coming loose and causing all those problems in the driving of the train.
Suggested correction: As you yourself stated, the whole thing is likely a dream, where "normal" reality doesn't apply. In the "real world", the train would never be able to do any of the things that it does in the film.
Dream or not, it is still a stupidity of the train crew to not secure a pin that could work itself free of the controls of the locomotive.
Dreams are often unrealistic. There is no mistake.
The entry doesn't say anything about the entire trip to the North Pole being a dream.
Stupidity: The lead Predator got infected with a Xeno chestburster, and at the end of the movie, his body is shown on the ship with it bursting out. This is what sets up the sequel. However, the Predators have been coming to Earth for centuries, and they have also been hunting the Xenos for centuries and know their behaviours and breeding habits. They have X-ray capability and even use it in this film to show a human is infected. Yet they never scan his body before bringing it on their ship. And yes, I know there's the whole thing about them coming out victorious, it seems, and the other Predators likely would assume they were untouched. That doesn't make it not stupid that they still didn't scan his body to be sure, as they know what these things are capable of. And of course, in the sequel, that stupidity bites them in the ass.
Stupidity: Even though Hermione reminds them that they must not be seen after freeing Buckbeak, they fly toward the castle, whooping and cheering because they're flying. Then, they land in the courtyard of the castle, have a conversation, and then Sirius flies off with Buckbeak. Not the behavior of trying to remain unseen and unheard.