Plot hole: In the common route, Mariya explains that in her former idol group, Quasar, "Your dance position has nothing to do with skill. It's based on a popularity poll." However multiple times in different routes and parts of the story they cross paths with Kaori ignoring who she is. She is number 5 of Quasar, the overwhelmingly most popular group in Japan. It's absurd they wouldn't know one of the most popular performers of their industry, and direct rival.
Plot hole: When Cutter is talking to Doc while he's in innerspace, he asks Doc how long he's been there, and Doc responds,"About three seconds." Cutter has been there for a lot longer, so he exclaims, "Three seconds?!", and Doc replies, "An hour to you is a second out here." The problem with this is that they are both conversing at a normal rate. If Doc's statement rings true, they wouldn't be able to have a conversation like that because Cutter would appear to be talking incredibly slowly, and Doc would appear to be talking at light speed.
Plot hole: At the end of the bandicoot pursuit, Cortex teleports away to escape Evil Crash so why didn't he simply teleport away earlier?
Plot hole: In the prologue of King of Fighters 95, Iori Yagami acts surprised by the presence of Kyo Kusanagi and vows to participate to the tournament, in fact the rest of the intro is about how he gets roped into the tournament by surprise thanks to Geese's manipulations. But as he delivers those first lines, behind him there's a giant poster supposedly celebrating the past edition, with Iori himself - who was not even in tournament - fighting against Kyo.
Plot hole: Five Characters In Search Of An Author: The opening cutscene ends with all five members of the family entering the gates to Matt Groening's mansion and walking down the path. Another cutscene then begins to play that continues on immediately after the previous cutscene where Homer and Bart are outside the mansion, but Marge, Lisa and Maggie are nowhere in sight. Since this cutscene continued on right where the previous one left off, there's no way they could have split up so quickly.