Stupidity: When Greg volunteers to watch the security monitors to see if the creatures can affect people through a screen, no-one even thinks to remain in the room with him to cover up the monitors with a blanket, towel or something similar in case the creatures' power can be transmitted that way. They tied him to a chair to reduce his chances of committing suicide, so they certainly thought there was a possibility that he would be in danger.
Stupidity: Why does the team choose to enter the shimmer from Area X and then trek for miles to the lighthouse? They could travel by sea and stage an amphibious landing on the shore right at the foot of the lighthouse. Obviously this would make for a very short movie, but this choice still needs to be explained in the plot.
Suggested correction: I thought it was an obvious tactical choice to go by land. If the mysterious shimmer radiates in all directions for miles, as it seems to in the movie, then it would also radiate for miles out to sea. A recon team is going to have a lot more options to deal with any "weirdness" on the ground rather than on a boat or in the water. (Also, the book "Annihilation" on which the movie is based makes it clear that there are some really big, nasty things swimming around in the water!).
Stupidity: At the very beginning of the movie, law enforcement is depicted executing a no-knock warrant. They approach a house surreptitiously and use a ram to open the door with no warning. When they arrived at the scene, all the cars and trucks in the raid were using flashing lights and wailing sirens. So much for the element of surprise.
Stupidity: After Roy escaped from the factory, he encountered a metal garage-door-type gate that was open at the bottom to the height of his knees. Trying to sneak away and in obvious pain from his injuries, it would have been quicker, quieter, and probably less painful if he crawled through the opening. Instead, Roy pulled downward on the chains, making a lot of noise, and it didn't even get the gate halfway up before he bent over to get out. The gate went up more after he stopped pulling on the chain. (01:15:29)
Stupidity: The metro police officer (and co-conspirator) went to the old cement factory where the other bank robbers were. Since the police officer (accomplice) wanted the money and did not want other police officers to be nearby, he called 911 and made an anonymous false report stating he spotted the person police were looking for and misdirected them further away. Maybe a good idea, but he made this call using his own cell phone. (01:12:20)
Stupidity: At the end of the movie during the shootout. Cops would not engage in automatic gun fire with dozens of civilians in direct cross fire. Why not get a chopper and chase them down a bit maybe in an open area with fewer civilians? Then maybe engage in gunfire.
Stupidity: Outside the bank, Mike and the first merc are having a shoot out across the parking lot. There is lots of room between them and around them. Yet a random construction worker, with a clear view of this shoot out happening, suddenly decides to take off running into the line of fire between the cops and the robbers and gets shot in the leg. Their was no reason for him to suddenly decide to run between them shooting at each other into the line of fire. (00:44:35)
Stupidity: Stephanie empties Emily's large closet, but when she comes back with the movers, lo and behold, all of the dead person's belongings are back. They are back though exactly as they were with superhuman inch-perfect precision. Since this movie does not have a supernatural element, that appears really silly. (01:00:30)