Young Kidaichi's Murder: File 1 - S2-E1
Other mistake: Miyuki notices the pager beeping and finds out that Kindaichi gave it to her without her noticing. In fact when he said goodbye to her, the keen-eyed viewer can actually spot him slipping her the device. There are a couple of slight problems with that; first, she retrieves it, not in frame, from her left side, but Kindaichi put it on the right side of her person. Second; she is wearing a white skirt with no pockets. (00:20:15)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: When Aoi repeats the question to the old servant, she has her hand on the lady's shoulder in the first shot, suddenly not in the second. (00:17:55)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: Reviewing Saki's footage of the evening of the murder, the part that shows Natsume is taken from an angle much closer than what it should be; Saki was sitting at the other end of the couch, not directly to her left. (00:17:00)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: Kindaichi and Miyuki are having breakfast since he already cracked the code but does not want to reveal the solution yet. A few seconds later there's a shot of the table from above the shoulder; not only the stuff on Kindaichi's tray changed and the yogurt moved to the right, but Miyuki was sitting across him and now she's on his right. (00:09:45)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: The close-up of the hot beverage cup doesn't match Itsuki's nor Miyuki's, since the complementary glass of water is on the wrong side. (00:03:40)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: When Miyuki waves at Kindaichi, her hair is in front of the left shoulder, behind the shoulder in the rest of the scene. (00:02:50)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: Across the 4 parts of the episode, both Kindaichi's yellow shirt and Miyuki's orange top are tie-fronts; the way they are drawn though keeps changing, and multiple times (would be redundant to enumerate them) they leave a large opening below the tie in one shot, and are completely closed in the next.
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: Kindaichi's teacher has a book rolled in his hand in a pattern that changes between shots. (00:02:25)
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 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 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
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
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: 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 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 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)
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 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)
Hikou Isle Murder Case: File 3 - S1-E15
Continuity mistake: When Kindaichi strips Midori, he yanks the bra completely off the breast bringing it all the way below the ribcage. That's in the front views, because in the back view merely the shoulder strap is lowered, the rest of the undergarment is perfectly horizontal and unperturbed.