Magical Express Murder Case: File 4 - S2-E13
Plot hole: The ending twist is nonsensical; the disciples have been using the tricks in Reiko Chikamiya's notebook for over 5 years, so the 'trap' inside the notebook could, and should, have happened at any point during that time. There's nothing in the killer's actions that makes that particular magic trick happen, nor he swapped or manipulated it.
Murderous Intent of Below Freezing 15 Degrees - S2-E9
Plot hole: Kindaichi's explanation of the trick does not make sense; he says the culprit put the towels outside to freeze in the bin, but if they were frozen solid they would have been impossible to reshape easily and quickly, and if they were already in the shape they wanted, that would have been just too big for the bin to contain. (00:14:25)