Academy's Seven Mysteries Murder Case: File 1 - S1-E1
Other mistake: Miyuki dirties her hand with ketchup leaning against a wall; however, the white wall has no red markings. (00:04:00)
Academy's Seven Mysteries Murder Case: File 2 - S1-E2
Other mistake: Kindaichi is afraid something might have happened to Miyuki. Finding blood, he has a flashback with several images about her. The final one though, the one with her sticking her tongue out and making a funny face, is something he can't reminisce about, since he wasn't there at the time. (00:18:40 - 00:21:00)
Academy's Seven Mysteries Murder Case: File 3 - S1-E3
Other mistake: The beginning of this episode does not match the previous one; Saki at the climax of the previous episode asked "Is that blood?" filming the scene, standing behind Hajime. In this episode he asks that when Kindaichi already turned around and grabbed him by the neck. (00:01:50 - 00:21:10)
Wax Doll Castle Murder Case: File 1 - S1-E7
Other mistake: Everyone rushes to Miyuki's position when she screams having found the first "victim." However, she screamed a while before already when Kindaichi scared her, and nobody ran to her then.
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.
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)
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.
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 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
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)
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
Other mistake: Kindaichi escapes handcuffing the detective to the toilet's chain. Try to think of the last time you went to a restroom and the chain was SO long that you could yank it across the whole room (not stall, room) and outside the door. Going behind the sink's drain, even. Never seen a toilet like this in my life (and in that kind of bathroom, you have usually buttons or pedals, anyway). (00:21:00)
Young Kidaichi's Murder: File 2 - S2-E2
Other mistake: Tokitou trips after charging at Kindaichi and missing him. Somehow though, Kindaichi is still way ahead of him and picks comfortably the lead pipe that rolled forward. (00:11:30)
Young Kidaichi's Murder: File 2 - S2-E2
Other mistake: Kindaichi is on the run from the police. He rolled in dirt with his only shirt and jeans, and he had multiple dirt stains when he was on the phone with Miyuki in Nagano, but at the end of his clandestine trip in the back of a truck, he shows up in Tokyo perfectly clean.
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: In the initial flashback, the name of the ship ("Mary Celeste") is misspelled, appearing on the stern, is "Mary Celese." (00:02:05)
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: When the two horrible guys harass her, Miyuki and Kenmochi are both drinking wine. Miyuki is underage, and while certainly not technically and materially impossible for someone underage to drink wine even with a police officer present, in pretty much every episode when there's a party it is made clear both in dialogues and visually that underage characters are not having alcohol. They drew the wrong type of glass. (00:08:45)
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: Everyone present in the scene reacts to Kenmochi popping the police inspector badge out of his jacket pocket. That includes the female crewmember who is peeking from the corner behind Kenmochi and that can't see it at all. (00:18:00)
Ghost Passenger Ship Murder Case: File 3 - S2-E7
Other mistake: The most the characters do after diving to rescue the suicidal girl is Kenmochi taking off his shirt. Kindaichi keeps his clothes and shoes, and Mizusaki even has his tie fastened as if nothing happened. They all have plenty opportunities to change clothes as they have their full luggage, but they don't, and they are just fine drying out from one scene to the next.