The Return of Hydro-Man: Part 1 - S5-E7
Stupidity: When Spider-Man is working in the lab, he uses his webbing to barricade the door shut so no-one interrupts him. When Debra Whitman shows up and asks who is in there, he identifies himself as Peter Parker. When he is finished with his work, he leaves out of the window so that by the time the security guards break the door down, he has vanished. Since he used his webbing to keep the door closed, it would be pretty easy for Debra and the security guards to figure out that Peter is Spider-Man since Spider-Man's webbing is at the scene and Peter seemingly vanished into thin air.
Behold, a Distant Star - S2-E10
Stupidity: When Johnny finds out his father is alive and wanted for murder, he is livid with his sister for telling him neither fact. When Sue decides to tell him the whole story, she asks Reed to pull a photo album from the drawer next to him, which contains a newspaper clipping detailing that their father was wanted for murder. If Sue didn't want Johnny to know about that, she shouldn't have placed the clipping in a photo album, and then kept the photo album in a communal area where Johnny could have easily discovered it at any time. (00:06:19 - 00:07:34)
Origin of Iron Man: Part 2 - S1-E12
Stupidity: When Mandarin is eavesdropping on what he believes to be Tony Stark and Yinsen eating their bowls of rice, but is actually a hologram, Stark remarks that it won't fool him for long. The hologram is nothing more than a static image of the two holding their bowls up to their mouths. The Mandarin shouldn't have been fooled by it all, considering they never move a muscle or consume any of the rice near their mouths. (00:11:49)