Stupidity: They go to great pains to lock the nodes behind an explosive lock, then have a debate about whether Riddick's somehow broken in. They eventually unlock them, check they're still in place...then just leave the locker completely unattended and unlocked while they discuss plans, and Riddick of course steals the nodes.
Stupidity: There are numerous snipers on and around the White House. They should have barraged the lawn and wiped out all the attackers on foot with rifles and machine gun fire.
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: A trained CIA hitman wants to kill the owner of a bar. Why would he go into the bar during opening hours, ensuring that there are witnesses to be eliminated, when he could break in after hours, use a few less bullets, and have fewer loose ends to tie up? The break-in would also provide a cover story for the kill. All rather unprofessional.
Stupidity: The security system is able to automatically ascertain the malfunction to the exact valve, and the electrical problem, but the alarm is not triggered at that point, but only when the holding cells are already filled with water and Breslin is making his return. They are on a ship, the fact that it's taking on water feels like a pretty important issue to monitor.