Returning Japanese (1) - S6-E21
Plot hole: In this episode, Hank meets his paternal half brother. They look alike. However, we saw in an earlier episode that Hank's facial structure takes after his mother, not his father. Since they are paternal half brothers, then the Japanese brother cannot look like Hank since he has a different mother.
Plot hole: Whenever Gretchin calls Mikey up to the stand to explain what he saw, he says that he had followed Spinelli and Randall to the wooden fence, where he Saw Randall on his knees in front of Spinelli, begging for forgiveness, then Mikey began running to the other side to stop Spinelli from pummeling Randall with the "rock" but didn't make it in time. We then later find out that Spinelli had actually rescued Ms. Finster's cat out of a tree and Randall hit himself with the rock out of spite. But it is impossible that Spinelli could have given up on hurting Randall, climbed up a tree, rescued a cat, climbed down, handed the cat back to Ms. Finster, gotten praise from Ms. Finster, then have Randall attempt to pick up a big rock, then get a smaller one and hit himself with it in under 3 seconds (the duration of how long Mikey ran before he heard Randall's scream).
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.
Plot hole: Throughout the series, Sandy always refers to Daria as "Quinn's cousin" or "that girl that lives with Quinn" or other random titles for Daria (not knowing that Daria is Quinn's sister). Although Quinn admits to Sandy that Daria is really her sister in one of the last episodes of the final season, in this first episode of the series, Sandy is in the crowd watching Daria give a speech and Daria reveals to everyone Quinn is her sister (embarrassing Quinn). Sandy should already know they're sisters.
Plot hole: During Ryder's report, as Bruce and company watch it on TV, the camera suddenly zooms in on Joker standing on a catwalk above Ryder, and none of the crew, especially not the camera man who caught the villain, makes a comment about this. They may have thought the Joker (or rather an impersonator) was perhaps a surprise gag in the show, but since this is supposed to be a serious documentary report, it is still strange that they wouldn't point it out.