Hiren Lake Legend Murder Case: File 3 - S1-E6
Plot hole: The plan of the killer relies on a couple of pretty strong coincidences, such as the fact that they wouldn't realise their common link (he knows nothing about what happened on the cruise, so he couldn't know that they all wouldn't realise they have met before) and the fact that the boat is discovered at the perfect time for him to commit murder (on someone who wasn't part of the trip, but is willing to join him).
Wax Doll Castle Murder Case: File 1 - S1-E7
Continuity mistake: When Miyuki tells Hajime that the winner of the contest will receive a castle, she's wearing a bag with a long and wide strap that happens to be colored exactly like her cyclamen shirt. In the rest of the scene she is carrying a pink and cream gym bag with short handles. (00:03:20)
Wax Doll Castle Murder Case: File 1 - S1-E7
Continuity mistake: When Miyuki notices that there's something in the doll's hand, it's an 8-ball, and there are two on the table. As the scene later shows, it's supposed to be a 6 ball, together with a 3 ball. (00:14:50)
Wax Doll Castle Murder Case: File 1 - S1-E7
Continuity mistake: When the party discovers the real corpse, the door physically knocks forward the 2 ball, which is on the floor. Later in the scene, the 2 ball rolls on the desk. (00:21:15)
Wax Doll Castle Murder Case: File 1 - S1-E7
Other mistake: Everyone rushes to Miyuki's position when she screams having found the first "victim." However, she screamed a while before already when Kindaichi scared her, and nobody ran to her then.
Wax Doll Castle Murder Case: File 2 - S1-E8
Continuity mistake: Hajime's towel changes color throughout the scene when he joins Miyuki and the inspector in the main room. (00:04:25)
Wax Doll Castle Murder Case: File 2 - S1-E8
Character mistake: Hajime's proposed solution is obviously wrong, but not for the reason they mention; the 'killer' could never clean themselves up completely and effortlessly in such a short time from the soot.
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.
Wax Doll Castle Murder Case: File 3 - S1-E9
Plot hole: Miyuki is not a detective or has any qualification in the world of crime novel. Her presence (taking up one of the 10 slots of detectives picked from all over the world, she's not an accessory to Kindaichi) is completely unexplained and nobody questions it at all.
Wax Doll Castle Murder Case: File 3 - S1-E9
Plot hole: According to what was established in the first episode of the arc, the statute of limitations for the crime has expired. In this third one though, it is said that they are afraid that the body will be discovered. There's no link between them and the victim (s), so to say that they joined the whole madness because they needed to prevent the castle from being 'moved' is absurd.
Gentleman Thief's Murder: File 1 - S1-E10
Continuity mistake: When the painting pops up with the card of the real Kaitou Gentleman's card on it, the card is placed on a different spot in the different shots. (00:11:55)
Gentleman Thief's Murder: File 1 - S1-E10
Other mistake: A single wimpy guy on his own wouldn't be able to bury something as large as a painting in a rush without leaving any trace the police can discover.
Gentleman Thief's Murder: File 3 - S1-E12
Character mistake: Itsuki tells Kindaichi about the painting the strange man was doing, saying it was "My Beloved Daughter." That is incorrect though, since what Itsuki would have been able to gather from the hospital staff was that the man painted lavender fields literally all over the room. The staff would remember that (a whole room of the building was changed!) and not that specific painting - and if they knew about it, news of it would have spread, being one of the most famous paintings in the world.
Hikou Isle Murder Case: File 1 - S1-E13
Other mistake: Miyuki manages to pinch Kindaichi's buttcheek while being in front of him, at an impossible angle. (00:06:45)
Hikou Isle Murder Case: File 3 - S1-E15
Other mistake: The cop shoots a hole through the box she's carrying - but there's the small detail that there's no opening at the back of it for her to stick the hand into and/or pull the trigger. (00:14:00)
Hikou Isle Murder Case: File 3 - S1-E15
Continuity mistake: When Kindaichi strips Midori, he yanks the bra completely off the breast bringing it all the way below the ribcage. That's in the front views, because in the back view merely the shoulder strap is lowered, the rest of the undergarment is perfectly horizontal and unperturbed.
Hikou Isle Murder Case: File 3 - S1-E15
Other mistake: A copper alloy statue knocks away like nothing a huge mass of gold ingots; gold is much heavier than copper, cumulatively the ingots weigh much more, and even if being simply piled on one another would cause them to be moved as the statue topples, it would never simply breeze through them.
Demon Suite Murder Case: File 1 - S1-E16
Continuity mistake: In the second murder, the toy tops on the floor are in a different position depending on the shot. (00:12:55)