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.