Stupidity: Even assuming that running in flipflops down the gravel road would give the culprit the required advantage over Kenmochi and Kindaichi, the culprit still had to run the elaborate setup in an absurdly short amount of time without leaving behind a single piece of gravel or wet stain (he was elbow deep in water) and hope nobody would set foot in the courtyard during the commotion.
Stupidity: The whole gimmick of this story is fun but it's pure anime nonsense; we have a 28 years guy who has spent 18 years of his life in complete darkness and malnourished. The effect of this (a stunted growth) is somewhat plausible in general, but in here he still has the appearance of the cute 10-years-old kid who was locked in the dungeon, he's athletic and a charming, fluent speaker. I don't think it's much-needed to elaborate on how that is laughable (although to be fair at least they mention that he'd light a lamp two hours a day to read and was 'exercising', which since all he ate was rats and had no sunlight at all, wouldn't quite have done him a lot of good).
Stupidity: Towards the end of the season, the Borg Queen uses Soong to get control of the ship. When asked by the heroes who gained back control, she says that her plan is to get back to the Delta Quadrant and prepare for the Confederation that she already fought in her 'future'. If that's her plan, it's quite silly; she prepares for a conflict she might lose, when she has in her grasp the man who, as she knows, will originate the Confederation itself; Soong, not to mention that she can assimilate (or destroy) the whole Earth already. No reason is given why she'd let 'us' live and thrive.
Stupidity: Since "Touno" was prominently featured on the photo of a lengthy article about the butterfly crypto-entomologist Shimon Madarame, it's quite strange to say the least that Kindaichi and his journalist friend wouldn't have the slightest clue about his name or generic occupation. Generally a magazine does not put a person in 1/3 of a double page spread without at least hinting the reader about a person's identity, especially when they are not doing anything in the picture.
Stupidity: The killer's plan is rather clever, but there's a huge hole in it; assuming the killer needs to be part of the game to set up the traps, there's absolutely no reason for the person they want to -benefit - from the crime to be part of the game. In fact, it is absolutely crazy; they were not involved at all, ignoring who the victim was, and if you wanted them to inherit from the victim, you'd want them to be MILES away from the crime instead of endangering them and inevitably implicate them. If all went smoothly, the police and media would surely have been on their case for the huge coincidence; they survive a murder and inherit from the victim of said murder.
Stupidity: Wanda's kids when she is possessed by the Scarlet Witch notice that she is walking two feet away from the sink and assume that she's going somewhere, but they didn't react at all to her breaking dishes, staggering, the lights flickering and the lamp moving wildly, etc.
Stupidity: To make the hit, The Killer places a bomb on the ceiling of his room - which is the floor of the victim's. He has absolutely no way to know where in the room the man will stand and when we see the explosion, it does not even touch the couch. The brilliant plan of the flawless killer is anything but brilliant or flawless.
Stupidity: The movie plot has a level of basic idiocy that the anime never had in any of its incarnations; Mr. X here is a scientist who made 3 unique masks that can be worn only by certain people with specific potential that are born"once in a lifetime", and raised 3 candidates out of maybe hundreds, for over 10 years of arduous training. One of them, Jo, out of jealousy attacks and cripples another. The mad scientist does absolutely nothing to stop the fight, that goes on for ages, nor punishes the rebel who did irreparable damage; in fact that aspect is never addressed at all and is as a normal case of "survival of the fittest." Later in the movie, Jo asks "permission" to hunt the third Tiger Mask, who meanwhile escaped. He didn't ask permission to destroy the most valuable asset of the gang, but he does for going after the traitor. X is also money-motivated and in a cutthroat competition against other branches, making his actions and inactions even more incomprehensible.
Stupidity: Naoto could have easily prevented his friend being crippled by their rival if just he put his superpower mask on, which he had with him all the time and tries to use only at the very end after Jo has been torturing Dan for a long time.
Stupidity: A world-famous painter known to be anti-social dies in a plane crash with other passengers in Hokkaido, Japan. The first responders are 4 reporters, one of which recognizes the corpse at first glance. They bury the body and one of them, on the spot and with no preparation, decides to impersonate him pretending to have burn marks on his face and going on wearing a surgical mask and a wig for 10 years. This has so many logical flaws; for this plan to work, the police had to never ask him anything, check his health after being the sole survivor of an airline tragedy, and the painter needed to have absolutely nobody who'd recognize his voice or know him at all.
Stupidity: The finale is sweet, but also the ultimate stupidity; there was a recording of the victim completely discharging one of the suspects from any blame, the recording was in one of the key evidences found by the police and used in the trial, but nobody ever played that recording. At least two families have to sue the State for a horrible job.
Stupidity: The denouement in this episode does not make any sense. Two characters (the lawyer, the victim's sister) are suddenly present on the scene for the climax, but they were never invited and if they were at the hospital in the corridor right at that moment, Busujima could not sneak by Kenmochi's room. Later Kindaichi gingerly explains the rest at the other crime scene, which is in a different building somewhere else in the city - and they are all physically there, even the patients in their hospital gowns and slippers, it's not a dramatic rendition.
Stupidity: Ramon's tail is strong enough to practically pancake a big limo, but at the same time David is hit by it, thrown against a solid brick wall, and is completely fine.(01:22:20)
Stupidity: For Sarah's murder to work, a lot of coincidences and unpredictable, convenient behaviour from the victim have to happen; she has to Miss the security guard and not hear them, she has to seek shelter of all places right in the costume room full of effigies of the killer, where the killer himself happens to be posing, she has to be completely inefficient at calling help with her cell phone.
Stupidity: Kindaichi's logic as usual proves to be right, however, the theater is surrounded by a pond, not the ocean. The investigation proceeds assuming that the killer who performed a meticulously premeditated murder with great knowledge of technology and conjuring, could never go past a bit of water. Likewise, they say "nobody left their seats since the lights go off", as a certainty, but watching the scene and how it unfolds, it's simply an assumption the plot needs.
Stupidity: Kindaichi and the others are called up by Satomi, who is one of the performers, so they can be in attendance for the show. They don't get changed, but somehow they are so late for the show that they are the last people to arrive, and the show is already ongoing and displaying the most famous act. If Satomi warned them late, makes no sense that he wouldn't be in the theater to begin with.
Stupidity: Lupin gets to the submarine diving from the plane Jigen is piloting. At the end of the episode Jigen is with him on the raft, with no mention of how and why he ended up like that.(00:22:50)
Stupidity: Despite the fact that there are 100 (literally) cameras around the racing circuit and (again literally) everyone from the staff to the fellow racers works for the Scorpion gang, Jigen and Lupin's switch can happen without anyone noticing, even if it involved racing side by side for a lengthy period of time.
Stupidity: Arashi tells Hoshino through his radio to call the HQ, but as shown several times throughout the show, his radio is perfectly able to do that directly himself. Even in this very episode later Hayata uses the standard issue radio to let the HQ hear the alien's requests.(00:07:20)