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)
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 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)
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)
Hida Mechanical Mansion Murder Case: File 1 - S1-E18
Continuity mistake: When Shino puts her hand on her mouth witnessing the disfigured face of Akanuma, her sleeve covers her face differently between shots. (00:18:20)
Hida Mechanical Mansion Murder Case: File 3 - S1-E20
Plot hole: The plot is based on the fact that a certain character was disguised as the presumed first victim. At the same time, the two characters have a different body type (otherwise the gap in the window would be obviously too small), so the turn of events does not make sense. Moreover, supposedly the victim suffered serious burns in a fire, which would be absent in the corpse.
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.
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)
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)
Opera House Murder Case: File 1 - S1-E21
Other mistake: Kindaichi and Miyuki are chatting with the lead actor who is sipping a Coke. There's a fierce argument onstage between the actresses; somehow the actor, in full stage garb, calmly shows up onstage to catch the end of the argument way before the other two kids get in the room running. (00:10:00)
Opera House Murder Case: File 1 - S1-E21
Character mistake: The brother of the dead actress, Fuyuko Tsukishima, stares intently at her diary. On its cover; "F. Tukishima", missing the S. (00:12:45)
Opera House Murder Case: File 2 - S1-E22
Other mistake: At the beginning of the episode, the characters are gathered thinking back about part 1 of the case. Amazingly enough, the propmaster's armpit ate the A of his shirt. Now he's not a "BADMAN", he's a "BADMN." (00:02:05)
Opera House Murder Case: File 2 - S1-E22
Continuity mistake: There's a blatant coloring error regarding Kindaichi's clothes when he speaks to the inn's manager through the window; his shirt goes from orange to lilac, with a pea green undershirt. (00:09:05)
Opera House Murder Case: File 2 - S1-E22
Other mistake: When Okata discovers the clue about the first murder in the recording room, the shadow cast in close-up is different from the wider angle - and it's also an impossible one, because the only light in the room is the one of her own flashlight, which couldn't be angled at the trolley that way. (00:11:25)
Opera House Murder Case: File 2 - S1-E22
Other mistake: In the flashback with the sulphuric acid bottle dropping on Fuyuko, the bottle has still the cap on, making the incident as it is shown impossible. It should also be noted that there's a shattered glass noise, but in the previous episode we saw the bottle was perfectly intact on the floor and was even reused for a murder (although how could the culprit be in possession of it is a mystery - it's the same one since the stain on the label is identical). (00:15:55)
Opera House Murder Case: File 2 - S1-E22
Character mistake: Like the previous episode, Fuyuko Tsukishima's name is transliterated wrongly in "Tukishima" on the cover of the diary.
Opera House Murder Case: File 3 - S1-E23
Plot hole: For Kiryu's murder, the killer's trick consisted in the fact that he wore her shoes after hanging her with a cable while she looked down from the window. First of all, it would have never worked as shown and the cable would have clutched her shoulders and arms rather than wrapping around the perfect spot on her neck to trick people to think she was hanged. Second, she was in her room and most likely not wearing shoes, thirdly; he'd still would have left a mark putting her shoes on unless he did it in midair, but still unless she had unusually big feet they would have never fitted him, and he couldn't leave the perfect prints that resulted.
Opera House Murder Case: File 3 - S1-E23
Plot hole: In the first episode, Hidaka screamed twice, but nobody heard the first scream, and everyone instantly came when they heard the second, but couldn't hear the sound of the crashing chandelier. She herself did not hear the alarm bell, but that is explained; trouble is, the fact that a curtain could make the stage totally soundproof is just impossible. A thick stage curtain can dampen the noise but not nullify it.
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.