Opera House Murder Case: File 3 - S1-E23
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.
Opera House Murder Case: File 3 - S1-E23
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.
Opera House Murder Case: File 3 - S1-E23
Plot hole: So the culprit checked in at a hotel without any document or... face, left the room right away using an inflatable boat contained in a medium size suitcase (which he left in the room) and with that reached the coast - because the hotel is on an island so remote that it took a relatively long trip by ship for the others to reach it. It's a plan all kinds of ludicrous and impossible - that's also without considering the fact that the hotel was booked by the cast of a Phantom of the Opera play and the staff knows the play, and one person hiding their face completely would be a pretty big coincidence they make nothing of.
Opera House Murder Case: File 3 - S1-E23
Plot hole: For the murder to happen, the killer needed to be next to the alarm bell and at the same time up in the stage rafter to cut the support cable, all while making sure the victim stayed exactly on the spot she needed to be for this demented trap to work.