Young Kidaichi's Murder: File 4 - S2-E4
Factual error: The bittersweet ending is powerful from a dramatic point of view, but also impossible, because law (in Japan, at least) explicitly forbids organs coming from suicide victims to go to their family members, to prevent behaviour exactly like the one displayed here.
Wax Doll Castle Murder Case: File 3 - S1-E9
Factual error: The culprit merely drops a chandelier from the ceiling in an unplanned move. From that simple action, the whole building - a huge castle - catches fire so quickly you'd think it's made out of papier-mâche soaked in gasoline, not stone.
Yukiyasha Legend Murder Case: File 3 - S2-E16
Factual error: Kindaichi begins his revelations at 4:10, and the time gradually shifts at 4:20 (which is a bit much for the amount of information revealed and the dynamics of the conversation, but okay). He then moves to the river, which is a couple minutes away from the house by car, to deliver the rest of his speech, and the sun dawns at that moment. It's a Japanese winter with -20 C°, the sun surely wouldn't rise at 4 AM. (00:06:30 - 00:12:00)
Magical Express Murder Case: File 4 - S2-E13
Factual error: The Puppeteer from Hell in flashback is training in Italy, but the magazine they give him with the news opens Japanese-style. (00:13:35)
