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 5 - S1-E14
Continuity mistake: When the mastermind does his dramatic escape, the policemen are in front of him (Kenmochi literally at arm's length), but there's nobody in his way when he throws his projectile. (00:18:15)
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.
Murder at 10,000 Meters File 1 - S1-E15
Continuity mistake: Kenmochi hands Kindaichi the ticket. The ticket, as you can see by the black stripe, is facing the opposite way between shots. (00:03:50)
Murder at 10,000 Meters File 1 - S1-E15
Continuity mistake: Kenmochi is holding the handkerchief in different ways when he calls Akechi after discovering the smoke bombs. (00:11:30)
Murder at 10,000 Meters File 1 - S1-E15
Continuity mistake: The captain's cap is on a different spot on top of the control panel when the investigators first see his body.
Murder at 10,000 Meters File 1 - S1-E15
Other mistake: In several instances throughout the episodes, the seats in the corridors appear empty even if the plane is supposed to be at full capacity.
Murder at 10,000 Meters File 1 - S1-E15
Other mistake: On the plane, Akechi is reading, according to the dialogue, an "English newspaper." The newspaper is called "Global Times", but it's not supposed to be the real life one, which is a Chinese newspaper (albeit with an english edition); the logo is different. However, for being a Western-style newspaper (which is what Kindaichi calls Akechi out for), its front page is positioned wrong, like a Japanese newspaper.
Murder at 10,000 Meters File 2 - S1-E16
Continuity mistake: Throughout the episode, number and position of the airplane windows vary. You don't have to freeze-frame and count them; a cursory look at the door at the center of the plane is enough. The way the windows by it are grouped together changes in number and the door is sometimes at the end of the line, sometimes in the middle of it.
The Campground 'Bizarre' Case - S1-E17
Audio problem: Having reached the campground sign, Juri Takano shouts at the others that they are almost there. Her mouth animation comes about a second before the sound starts. (00:06:50)
The Campground 'Bizarre' Case - S1-E17
Continuity mistake: When Kindaichi's friend suggests washing their clothes in the river, Kindaichi's fishline spirals around the rod in a different manner between shots. (00:09:00)
The Campground 'Bizarre' Case - S1-E17
Continuity mistake: When Miyuki discovers the larceny perpetrated at her expense, proportion and position of the folded clothes change between shots. (00:10:45)
The Campground 'Bizarre' Case - S1-E17
Deliberate mistake: The evidence that proves Kindaichi's alibi is the store receipt detailing the time of his purchase. Notice that the year is recorded too, but it reads "20XY." (00:12:40)
The Campground 'Bizarre' Case - S1-E17
Continuity mistake: When Kindaichi tries to escape and Miyuki stops him in his tracks exposing the reason why he's leaving, the cup in front of her is positioned with the handle facing right. When we see the cup again, it faces the opposite direction. (00:21:20)
Evil Spirit of the Diving Pool - S1-E18
Continuity mistake: When Miyuki says that Honosuke the owl is cute, all we see in her glass is an ice cube. Moments later, her glass is filled with orange juice, the ice cubes being well below the juice level. (00:02:15)
Evil Spirit of the Diving Pool - S1-E18
Continuity mistake: At the beginning of the flashback from three years prior, Miyuki pounds the top of Hajime's head with a righteous fist. At the cut, he has his left hand up, while in the first shot it was lowered. (00:03:15)
Evil Spirit of the Diving Pool - S1-E18
Continuity mistake: In the scene with two swimmers having a physical altercation, the bag of 'the ripper' is in a different spot on the bench between shots. (00:05:30)
Evil Spirit of the Diving Pool - S1-E18
Other mistake: Kindaichi is watching poolside the athletes on day two. He is sitting cross-legged, but his right foot is drawn wrong and the toe is twisted in an impossible position. (00:08:10)
Evil Spirit of the Diving Pool - S1-E18
Continuity mistake: 14-years old Kindaichi comes up with the solution of the case but gets interrupted as he is about to utter his catchphrase. In the scene, the bookmark is in the top half of the book next to him, the bottom half when we see his mother scolding him. (00:12:00)
Evil Spirit of the Diving Pool - S1-E18
Continuity mistake: When Kindaichi wakes up from the flashback/dream, Miyuki stares at him with her fingers along her cheek or closed to a fist. (00:21:00)