Young Kidaichi's Murder: File 1 - S2-E1
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)
Young Kidaichi's Murder: File 1 - S2-E1
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)
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: When Miyuki waves at Kindaichi, her hair is in front of the left shoulder, behind the shoulder in the rest of the scene. (00:02:50)
Young Kidaichi's Murder: File 1 - S2-E1
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.
Young Kidaichi's Murder: File 1 - S2-E1
Continuity mistake: Kindaichi's teacher has a book rolled in his hand in a pattern that changes between shots. (00:02:25)
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)