Stupidity: When the invasion of planet P begins, we see the Rodger Young get hit. In the explosion sequence, we are treated to people sitting around tables in what can only be described as a mess hall exploding. In a military environment, this would be a time where everyone would be at their "battle stations". Nobody would be having chow or off-time when the ship is expecting combat. In this case, it was a planned troop landing.
Suggested correction: Yes, it was stupidity, but it was an intentional depiction that supports the plot. During the landing, the Captain is completely surprised by the bombardment and says something like, "This isn't light uncoordinated resistance." The fleet's lack of preparedness at Planet P is a major plot point that later results in the replacement of the Air Marshal in command.
No, you are talking about a different sequence. When they are unprepared, they are doing an invasion of Klendathu, the Bug's home planet. This is earlier in the movie and the Rodger Young was only slightly damaged in that. The stupidity is about the invasion of Planet P at the end of the movie, where the Rodger Young is cut in half.
Stupidity: After pushing the button for the outer door in the airlock, Justin was brought out of his trance. The door was on a delay, so why didn't he just go to the console and abort the door's opening?
Stupidity: Central to the plot is the layout of the Mars lander. There are no seats or any restraints of any kind in the lander, which is ridiculous. Spacecraft require safety belts in order to prevent astronauts from being injured during rapid course corrections. Additionally, ordinary rolling desk chairs would not be sent into space, and would certainly not be placed on a landing vehicle.