The Death March of Young Kindaichi File 2 - S2-E2
Plot hole: It's unreasonable, nor is explained in the denouement at the end of this arc, how did the murderer, who stayed behind everyone else on purpose, get to Shinomiya who was ahead of everyone, went inside the cave before everyone else and didn't have a reason to hide, cooperate with him or anything of the sort.
The Death March of Young Kindaichi File 3 - S2-E3
Plot hole: The crowd freaks out when Matsuoka's body is found and Kindaichi happens to be standing in front of it, gun in hand. That's all sorts of silly though, not only because the killer could have never predicted that turn of events, but also because Kindaichi roamed the streets looking for Matsuoka, gun in hand the whole time (it's a different gun from the one Matsuoka is killed with), and it's a girl screaming that draws everyone's attention to the murder. What about the two gunshots? Everyone in the background was entirely unfazed. It also creates a separate issue in the ending, since the plan to frame Kindaichi was supposed to be 'perfect' but the different gun would have spoiled it. (00:08:35)
The Death March of Young Kindaichi File 3 - S2-E3
Plot hole: Kindaichi bases his solution on a fact (there was a certain object on the elevator together with the victim) he couldn't know about, since Li did not mention it (and if he did, he would have been on the right track to solve the mystery himself).