Black Butterfly Murder Case: File 1 - S3-E1
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.
Yukiyasha Legend Murder Case: File 2 - S2-E15
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.
Magical Express Murder Case: File 2 - S2-E11
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.
Magical Express Murder Case: File 2 - S2-E11
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.
Young Kidaichi's Murder: File 2 - S2-E2
Stupidity: When Akechi tells his men to look for Kindaichi in all the possible places where a person might hide, Kindaichi with his bright yellow shirt is behind a metal staircase 2 meters away from him - a metal staircase with gaps between the steps, and some of the policemen are facing him. (00:20:15)
Young Kidaichi's Murder: File 1 - S2-E1
Stupidity: Kindaichi behaves in a criminally illogical way in this fourth parter episode. The original victim told 4 separate people some sort of keyword for the party, each one linking to another person. Kindaichi after at least the second if not the first victim could and should have asked EVERYONE (he had every opportunity for that) if they received such a 'password' by Tachibana before he died. Instead, he pointlessly follows the trail of breadcrumbs and two if not three people die for nothing.