Yukiyasha Legend Murder Case: File 1 - S2-E14
Other mistake: Throughout the whole three-parter, whenever the characters are in the snow, it comes down at really sharp (45°) angle with a whistling wind, but their hair and clothes are entirely unperturbed.
Magical Express Murder Case: File 1 - S2-E10
Other mistake: Flower petals continue raining down before and after Akechi picks up the rose from the ground, but never during his action. (00:16:10)
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: Everyone present in the scene reacts to Kenmochi popping the police inspector badge out of his jacket pocket. That includes the female crewmember who is peeking from the corner behind Kenmochi and that can't see it at all. (00:18:00)
Ghost Passenger Ship Murder Case: File 3 - S2-E7
Other mistake: The most the characters do after diving to rescue the suicidal girl is Kenmochi taking off his shirt. Kindaichi keeps his clothes and shoes, and Mizusaki even has his tie fastened as if nothing happened. They all have plenty opportunities to change clothes as they have their full luggage, but they don't, and they are just fine drying out from one scene to the next.
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: When the two horrible guys harass her, Miyuki and Kenmochi are both drinking wine. Miyuki is underage, and while certainly not technically and materially impossible for someone underage to drink wine even with a police officer present, in pretty much every episode when there's a party it is made clear both in dialogues and visually that underage characters are not having alcohol. They drew the wrong type of glass. (00:08:45)
Young Kidaichi's Murder: File 2 - S2-E2
Other mistake: Tokitou trips after charging at Kindaichi and missing him. Somehow though, Kindaichi is still way ahead of him and picks comfortably the lead pipe that rolled forward. (00:11:30)
Ghost Passenger Ship Murder Case: File 1 - S2-E5
Other mistake: In the initial flashback, the name of the ship ("Mary Celeste") is misspelled, appearing on the stern, is "Mary Celese." (00:02:05)
Young Kidaichi's Murder: File 2 - S2-E2
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.
Young Kidaichi's Murder: File 1 - S2-E1
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)
Young Kidaichi's Murder: File 1 - S2-E1
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)