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)
Demon Suite Murder Case: File 2 - S1-E17
Continuity mistake: When the butler arrives in the room where Arisa was wounded, the arrow in the foreground is at an impossible angle considering it should point towards him. (00:04:10)
Demon Suite Murder Case: File 1 - S1-E16
Continuity mistake: In the second murder, the toy tops on the floor are in a different position depending on the shot. (00:12:55)
Hikou Isle Murder Case: File 3 - S1-E15
Other mistake: The cop shoots a hole through the box she's carrying - but there's the small detail that there's no opening at the back of it for her to stick the hand into and/or pull the trigger. (00:14:00)
Hikou Isle Murder Case: File 3 - S1-E15
Other mistake: A copper alloy statue knocks away like nothing a huge mass of gold ingots; gold is much heavier than copper, cumulatively the ingots weigh much more, and even if being simply piled on one another would cause them to be moved as the statue topples, it would never simply breeze through them.
Gentleman Thief's Murder: File 3 - S1-E12
Character mistake: Itsuki tells Kindaichi about the painting the strange man was doing, saying it was "My Beloved Daughter." That is incorrect though, since what Itsuki would have been able to gather from the hospital staff was that the man painted lavender fields literally all over the room. The staff would remember that (a whole room of the building was changed!) and not that specific painting - and if they knew about it, news of it would have spread, being one of the most famous paintings in the world.
Gentleman Thief's Murder: File 1 - S1-E10
Continuity mistake: When the painting pops up with the card of the real Kaitou Gentleman's card on it, the card is placed on a different spot in the different shots. (00:11:55)
Gentleman Thief's Murder: File 1 - S1-E10
Other mistake: A single wimpy guy on his own wouldn't be able to bury something as large as a painting in a rush without leaving any trace the police can discover.