Continuity mistake: When Hajime is looking at the photo of the crime scene, the outline of the body is correct when it comes to the arms position, but the torso is straight, when it was very much bent in the first episode.(00:08:55)
Continuity mistake: Kindaichi's head peeks from the corner of the window at different levels when he spots the silly policeman getting stuck.(00:04:35)
Continuity mistake: Kindaichi is looking at the pictures he laid out on the train's floor. When we see the wide shot with all the pictures, they don't match any of the closer angle.(00:03:40)
Continuity mistake: Katsura gets stabbed in front of Kindaichi; Kindaichi's tie is missing part of the string as he calls Katsura's name the first time.(00:21:15)
Continuity mistake: The space between the steps of the metal staircase Kindaichi is (amazingly well) hiding changes between shots. In fact when the beeper beeps, the whole back of Kindaichi appears to be leaning on solid steel.(00:20:20)
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.
Continuity mistake: When Kindaichi pages Miyuki, she clicks the button on top to answer, but in the next shot she's holding the device in a different way.(00:04:15)
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)
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)
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)
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)
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)
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)
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.
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.
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.