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)
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)
Continuity mistake: When Miyuki discovers the larceny perpetrated at her expense, proportion and position of the folded clothes change between shots.(00:10:45)
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.
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.
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.
Stupidity: When the Puppeteer is shot, like any good villain he's actually wearing a bulletproof vest. However, a bulletproof vest is not a magical forcefield that neutralizes kinetic energy; this guy barely flinches when hit. Neither are flames; his fire trick raises a literal firewall, but firewalls are not literal walls, they do not stop bullets. The policemen could easily keep shooting through it (he throws a glove at Kindaichi through it), but they just do not, for no reason.
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)
Other mistake: Kindaichi puts on the table the map of the two buildings. The one to the right has a cutout part, but still shows as a full sheet.(00:19:00)
Stupidity: When Kirisawa's body is discovered, it means that he was completely overlooked during the headcount and at every point during the day. With students disappearing left and right, that's a pretty big oversight - that somehow the killer anticipated, because his body discovered last was crucial for the plan.
Continuity mistake: The burn marks on Adechi's tracksuit change throughout the episode. For instance, look at his left forearm; sometimes it has a dark spot, some other times it does not.(00:16:00 - 00:17:15)
Plot hole: Kujiragi's textbook is missing. It's a plot point and it's something the culprit did to plant an evidence using a page from it. However, when the case is solved, this point is glossed over; only a page from the book was needed, which the culprit could have ripped away at any moment without stealing the book, and more importantly, when Kindaichi finds the book, there was no window of opportunity for the killer to put it back; Kindaichi and Kujiragi were right there in the corridor the whole time. The live version adaptation fixes this hole because the character finds his book only the day after, in class.
Continuity mistake: Kujiragi grabs Kindaichi asking about his textbook; Kindaichi raises both hands almost putting them in the aggressor's face, but at the cut you get an unobstructed view of him; Kindaichi's arms are lowered.(00:05:00)
Character mistake: When we first see Kindaich in English glass, the blackboard behind the masked teacher shows the word "grammar" misspelled into "grammer."(00:12:10)
Continuity mistake: In the opening shot of the 'briefing' about the camp's structure, Kendaichi's backpack is twice the size it turns out to be in the rest of the scene.(00:03:20)
Stupidity: The whole story of the 5 episode arc requires unhealthy amounts of suspension of disbelief; the killer directly challenged the police and announced where and when the murders will take place; at a 3 days prep school camp. Despite that, one of the teachers, a new one at the job even, is allowed to attend the camp wearing a ski mask, supposedly to hide hideous burns, and the police just lets him in without checking. And yes, he's the criminal, not even a red herring. By comparison, in the live version adaptation they check him, and he's wearing prosthetic scars.
Continuity mistake: Once the Puppeteer disappears, you can't see Miyuki's glass and the box on the table any more either (but she has another table behind her when you see her hand in the foreground).(00:21:30)
Stupidity: Paragon of cleverness inspector Adechi somehow did not check for any trap in the mysterious box he received, and brought it to a crowded cafe just, so he could show it to the kids. For the explosive trick to work, the puppeteer needed also to know exactly where Kenmochi would be seated and which seats would later Kindaichi and Miyuki pick, since the box had to be at such an angle that the puppet would be propelled to the exact spot on the roof that acted as podium.
Continuity mistake: After the Puppeteer's speech, the box emits sparks. Adechi shields his face with his sleeve fully in close-up, while in the wider angle he is mouth agape with the arm positioned at a lower angle.(00:20:50)