Free Family Portrait Studio - S8-E24
Stupidity: Dwight is seen walking out of the bathroom with the diaper in the direction of the main part of the office in which Angela sits. If he was to try to stay hidden (which was obviously the whole point), he would have gone through the exit of the annex, waited until she was distracted/or hide it for later and Angela never would have seen. This was done because the plot required for Angela to notice but Dwight could have easily kept it hidden. (00:10:40)
The Signs in the Silence - S6-E21
Stupidity: Bones realises she could pull a wisdom tooth from Amy in order to identify where she grew up and find her birth parents. Which works, but at no point do they consider simply going through missing person records with the relevant info. They know how old she is, they know roughly when she disappeared, not like there are hundreds of 3 year olds going missing every year, especially not with Waardenburg syndrome. By that age her deafness would have been apparent, which would narrow the pool hugely.
Stupidity: When they are conferring before surgery everyone is keeping scrub except for Avery who has his arms crossed. Shortly afterwards you can see him look around at all his co-stars, realise he screwed up and try to casually raise his arms. (00:15:00)
Stupidity: During the scene at the restaurant, Rose pulls the fire alarm. Then she and the doctor run through the kitchen, past several chefs who just duck and crouch into corners. This would easily be one of the stupidest ideas ever. If there was a fire, they would evacuate out the back door instead of just sitting there waiting to be choked to death. And if they knew about Auton Mickey, running out the back door would also be a lot more logical than just crouching down and waiting to be battered to death.