Hikou Isle Murder Case: File 1 - S1-E13
Other mistake: Miyuki manages to pinch Kindaichi's buttcheek while being in front of him, at an impossible angle. (00:06:45)
Wax Doll Castle Murder Case: File 3 - S1-E9
Factual error: The culprit merely drops a chandelier from the ceiling in an unplanned move. From that simple action, the whole building - a huge castle - catches fire so quickly you'd think it's made out of papier-mâche soaked in gasoline, not stone.
Hiren Lake Legend Murder Case: File 2 - S1-E5
Continuity mistake: Eiji just left to get help through the lake. When Miyuki says "Not really" on the topic of jealousy, the sheets are pulled all the way up to her chin, but they are lower in the following shot. (00:06:45)
Hiren Lake Legend Murder Case: File 1 - S1-E4
Continuity mistake: When Kindaichi and the others talk with the mature couple, the president is wearing a purple-ish jacket and a red shirt. At dinner, they make a comment about Miyuki and Eiji Touno being a couple. From behind, the president is wearing his jacket, but from the front he's just wearing the red shirt. (00:09:40)
Hiren Lake Legend Murder Case: File 3 - S1-E6
Plot hole: As it often happens in this sort of murder mystery, there's a switching act at one point, and one of the 'disfigured bodies' is not who it is presumed to be. Good, but the problem is that the presumed victim and the person who really died have radically different skin tones, and it'd be practically impossible for anyone who knows them to mix them up - even moreso for the genius detective Hajime Kindaichi.
Academy's Seven Mysteries Murder Case: File 3 - S1-E3
Plot hole: A corpse has been buried inside the walls of the building for 10 years. It's covered by just a poster, and a poster from a current high schooler. If we assume the first victim was the one who put the poster there, then it means that it was just randomly uncovered by the earthquake from episode 1, which would make the chain of coincidences nothing short than miraculous. She basically one day said "I heard there was a murder here where we all hang out all the time" and the ground by its own accord opened to reveal a skeleton without her doing anything.
Academy's Seven Mysteries Murder Case: File 2 - S1-E2
Continuity mistake: Kenmochi puts his hand on Kindaichi's shoulder, open palm and full grip. A split-second later he's waving at him the police badge with the same hand. (00:02:00)
Academy's Seven Mysteries Murder Case: File 1 - S1-E1
Continuity mistake: Sakuragi hints that she knows Makabe's secret, and snubs him completely. He storms out and stumbles upon his ghost writer Tomoyo Takajima. She is wearing just a right glove, but when he backhands her, she is wearing gloves on both hands. (00:12:25)
Academy's Seven Mysteries Murder Case: File 1 - S1-E1
Continuity mistake: When Sakuragi hands Kindaichi the meeting minutes from 1987, the floppy disk is in a different position in the wider angle, and the book itself is headlined by two kanjis written vertically, instead of horizontally like in close-up. (00:10:35)
Opera House Murder Case: File 3 - S1-E23
Plot hole: So the culprit checked in at a hotel without any document or... face, left the room right away using an inflatable boat contained in a medium size suitcase (which he left in the room) and with that reached the coast - because the hotel is on an island so remote that it took a relatively long trip by ship for the others to reach it. It's a plan all kinds of ludicrous and impossible - that's also without considering the fact that the hotel was booked by the cast of a Phantom of the Opera play and the staff knows the play, and one person hiding their face completely would be a pretty big coincidence they make nothing of.
Opera House Murder Case: File 1 - S1-E21
Continuity mistake: Miyuki's hair is windswept in front of her neck at first, then behind her shoulders as she asks Hajime how he's feeling. (00:02:00)
Demon Suite Murder Case: File 1 - S1-E16
Continuity mistake: When Tsubaki exits Kure's room, the glass vanishes from his tray. (00:19:15)
Opera House Murder Case: File 3 - S1-E23
Plot hole: For the murder to happen, the killer needed to be next to the alarm bell and at the same time up in the stage rafter to cut the support cable, all while making sure the victim stayed exactly on the spot she needed to be for this demented trap to work.
Opera House Murder Case: File 1 - S1-E21
Continuity mistake: At the beginning of the episode you can see on the deck only Miyuki, a guy to her right, and to her left Kindaichi and her female friend. When Kindaichi starts throwing up, the whole drama club is there and everyone's position has changed. (00:01:45)
Hida Mechanical Mansion Murder Case: File 3 - S1-E20
Plot hole: Even considering the fact that the corridor was dimly lit (but not in complete darkness), it is impossible to plan the 'switch' the way it happened. For the plan to work, the killer needed to go through a revolving door at the same time as Kindaichi; there was no guarantee which of the two halves of the door he'd make spin, though, and he needed precise timing (against someone running through the door at full speed) and not make a sound with the keys he was carrying. The corridor (and therefore the door) is also so narrow that you wouldn't be able to ever pull it off.
Hida Mechanical Mansion Murder Case: File 1 - S1-E18
Plot hole: At the beginning of the episode, Kindaichi and his friends have an encounter with the mysterious figure that will be murdered later (allegedly). Three episodes later the identity of this mysterious figure is revealed, creating an impossibility when you consider who played that role. (00:03:10)
Demon Suite Murder Case: File 2 - S1-E17
Revealing mistake: When Kindaichi looks the name up in the French dictionary, the pages are entirely made up of the same paragraph repeated over and over. (00:08:50)
Demon Suite Murder Case: File 2 - S1-E17
Continuity mistake: Inside Arisa's room when she screams for the arrow incident, Miyuki's top is the same color as the sleeves of Kindaichi's polo, instead of being yellow. (00:04:00)