Stupidity: After the team break Solomon Lane out of custody, they drive around Paris with him in the front seat of their car. Lane is still wearing a straightjacket, bound in chains and has a black bag over his head. The IMF team drive him through crowded streets, past multiple police cars in full view of everyone just minutes after an armoured convoy transporting a dangerous prisoner (who everyone is now looking for) has been attacked. None of the Parisian police seem to notice this and none of the IMF team questions the tactical soundness of this approach.
Suggested correction: What's stupid about this approach? The IMF team is trusting that with their skills and experience they can easily evade any police that spot them. Which of course they do. Placing Lane in the trunk would have kept him out of sight but that doesn't really matter because they weren't planning on sneaking him out, they were planning on a quick escape.
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: They could've used the flying chopper thingy to kill off the armed guys when rescuing the kids off the train carriages. That way they could have made sure they got every single kid rather than rushing to just take the one containing Minho (which they messed up).
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: When Olivia said, "Momma. It's hot", she was wearing a long-sleeved shirt over her overalls and shirt. Her mom, wearing a sweater over a tunic top, replied, "I know, baby" and asked Steve to turn the A/C on in the RV, but the A/C didn't work. Instead of removing some layers, Steve opened some windows. Jay complained how hot it was, but he wore a hooded sleeveless sweatshirt over his T-shirt (and never took it off, even when outside in the desert). (00:09:31 - 00:46:00)
Stupidity: Milton, straddling Edie's body on the floor, is about to pull the plastic sheeting over her head. Edie's eyes suddenly open, and she starts screaming. Instead of quickly pulling the plastic sheeting over her head and suffocating her, Milton half-heartedly struggles to control Edie's hands, which she somehow manages to raise from alongside her body and around his to be in front of her neck. (00:38:50)
Stupidity: The building is supposed to be without power - at all since the generator has been destroyed - and life support machines are not powered up, but the 3D printers in every room are powered up - so that the good guy can squish the bad guy's head in it, and the elevators, so that the good guys can escape. What sort of hospital has its electric grid rigged in a way that the elevators keep working but critical surgical equipment goes dead the moment the power fails? (01:12:00)
Stupidity: While running "silently", the SONAR keeps beeping. Active SONAR is akin to yelling "Polo" in a pool.
Stupidity: The team raids the house and locates 5 people inside deemed to be Russian operatives. They are subdued and placed on their knees, while some of the team works on gathering intel from the home. The subjects should have been handcuffed/zip-tied. Since they were not they were able to grab stashed weapons and cause a gun fight which led to one of the entry team's members being killed and all the Russian operatives killed. It's common knowledge to restrain people. Cops and military always restrain. (00:04:00 - 00:12:00)