The Prison Prep School Murder Case File 1 - S1-E10
Revealing mistake: When Kindaichi and Miyuki speak with Kenmochi, inspector Adechi is lurking in the background reading what turns out to be a French newspaper. At the beginning you can see its "Le Shinbun" logo on both the front and back cover, but later in the scene it has just one cover and the back page is just normal text (incidentally, the filler text is garbage; the headline says "Je vais essayer de répondre l'incident" and even breaks the words incorrectly, but you have to freeze-frame to spot this last detail). (00:17:10)
The Prison Prep School Murder Case File 1 - S1-E10
Continuity mistake: When Kindaichi reveals that someone in the room probably is the responsible, Mizogishi asks in a shot from behind if anyone knows anything. In that shot, the two adjoined desks he was using become a single supersized table. (00:16:00)
The Prison Prep School Murder Case File 1 - S1-E10
Continuity mistake: When Mizogishi concludes his deduction, he puts the evidence bag down, and it is on the right desk, or on the left desk depending on the shot. (00:13:00)
The Prison Prep School Murder Case File 1 - S1-E10
Continuity mistake: During the interrogation scene there's a student with the same purple uniform Miyuki and Hitomi wear. She keeps switching sides, being next to the teachers or next to Hitomi, the latter being her wrong spot; the student next to Hitomi Kaidou is in other shots Yurika Enami, with her cream jacket. (00:09:00)
The Prison Prep School Murder Case File 1 - S1-E10
Continuity mistake: When detective Mizogishi begins his interrogation, the booklet inside the evidence bag is horizontal (longer side parallel to the longer side of the desk), then vertical (longer side perpendicular). (00:09:20)
The Prison Prep School Murder Case File 1 - S1-E10
Continuity mistake: Crazy-eyed Hitomi Kadou calls Kindaichi "dumb" out of the blue. Kindaichi is carrying his school bag over the right shoulder, but in the reaction shot his shoulder is clear. (00:06:05)
The Alchemy Murder Case File 4 - S1-E9
Continuity mistake: In the flashback when we see the culprit holding the newspaper with the news about the suicide, their thumb is on the blue box, which is at the edge of the page. Then they fall on their knees crying, and there's suddenly an extra bit of newspaper to the right of the box and their hand is on that. (00:15:15)
The Alchemy Murder Case File 3 - S1-E8
Plot hole: The locked room mystery is original, but besides the fact that it requires melting part of a door on the spot and being able to repair it absolutely flawlessly so that nobody would notice any bump and discolouring and irregularity when they check the lock later investigating the murder, it also requires them to do it in total silence so the other guests don't notice, and part of the process shown involved cutting through it with a screwdriver and bashing it with a hammer - they show that and there's even a loud sound effect for it. (00:18:00)
The Alchemy Murder Case File 3 - S1-E8
Factual error: The Latin text on the supposedly old tome (which is written with a modern font) displays an alchemist diagram. It is a reproduction of a famous drawing meant to portray the Philosopher Stone in the Sylva Philosophorum, but whoever copied it does not know Latin, because certain words are misspelled ("Merceralia" instead of "Mercurialia", "Humides" instead of "Humidus"). (00:10:10)
The Alchemy Murder Case File 3 - S1-E8
Continuity mistake: Mikage is startled by someone knocking at the door. She then puts the knife back on the desk when she realises who is it. The knife and the towel she partially hides it in are in the middle of the desk, but when they tell her that she is a likely target, the items are on the edge of the table. (00:05:10)
Reika Hayami and the Uninvited Guest - S1-E5
Continuity mistake: In the hall where Reika holds the quiz, the participants keep changing clothes throughout the scene depending on the camera angles.
The Hong Kong Kowloon Treasure Murder Case File 4 - S1-E4
Plot hole: Miyuki has been peacefully waiting for over a day at a stranger's house because she was told that the whole Hong Kong was under lockdown and her friends were in another location. That cover story (which would have been exposed if only she looked out of the window, people were NOT in lockdown) does not explain at all the kidnapping in the clothing stall or why she didn't have her phone or talk to Hajime at any point. She'd have to be braindead not to question even slightly what was happening.
The Hong Kong Kowloon Treasure Murder Case File 2 - S1-E2
Plot hole: An essential part of the plot relies on the fact that thanks to Saki's handheld camera, Kindaichi can examine Ran's arse dragon and therefore investigate even in her absence. But what set the plot in motion was the fact that Ran appeared in a professional modelling photoshoot displaying it. Stupidity of the girl aside, that means that the culprit never needed the girl, having HQ shots of the tattoo at their disposal. They even work for the company.
The Hong Kong Kowloon Treasure Murder Case File 1 - S1-E1
Continuity mistake: A mysterious man spills beverage on Miyuki's tanktop, creating a large brown stain that forces her to go change clothes. When she steps into the changing room from the urban legend, though, her clothes are pristine, the stain is entirely gone. (00:08:10 - 00:09:15)
The Prison Prep School Murder Case File 5 - S1-E14
Plot hole: The victim managed to write a dying message with chalk on the inside of the locker, but the only moment when he could have done that was when his assassin was standing there watching him die waiting to drag his corpse away. Since the writing was basically the killer's name, it's absurd that the killer never bothered to wipe out the signs; it's chalk on hard metal, not a single trace would have remained. It also does not match the position of his hand in the second episode.
The Prison Prep School Murder Case File 4 - S1-E13
Plot hole: The basic causality principle is reversed when explaining the murder with the corpse discovered on fire. The lesson was about combustion and took place before (or during, rather) the murder, so it couldn't be something used to disguise an unexpected problem that hadn't surfaced yet. Additionally, there's no reason why the murderer couldn't act as first responder or place the body near the river or in the bathroom.
The Prison Prep School Murder Case File 3 - S1-E12
Continuity mistake: When Kindaichi's classmate spots the corpse outside the window, he reacts putting a hand on his chest in the wide angles, on his mouth in the close-up. (00:14:15)
The Prison Prep School Murder Case File 3 - S1-E12
Audio problem: Someone "accidentally" drops an eraser, drawing the teacher's attention. It's a soft pencil eraser with no additional parts, but it falls with a clicking noise as if it were made of hard plastic. (00:08:30)
The Prison Prep School Murder Case File 3 - S1-E12
Continuity mistake: The "Sunlight" group is being tested on Dostoevsky's "Demons." In the aerial opening shot of the test, Kindaichi is not holding any pen (it's on the desk), but in the next shot he does. (00:08:25)
The Prison Prep School Murder Case File 3 - S1-E12
Continuity mistake: When Miyuki says that if they finish the test early, they will have a bit of time to relax, her pen is to the left of the paper. Close-up, and it's on the right side. (00:06:40)