Submarine Shrine in Lufia 2 has to be up there.
About 80% of the way into the game you get a sub and you go to this plot-crucial area, where Maxim finds the magic sword that the game revolves around, and where you meet the main villain for the first time.
Unfortunately both of those events are rendered incomprehensible by the fact the Submarine Shrine is completely fucked.
(bad quality, but there was nothing else)
It's just a bunch of junk data. If you go straight up you trigger the cutscene (which you can't even see), but there's no way to know that's what to do unless you check a guide. I think everyone thought they broke the game when they first entered here.
How the fuck do you let something like that go to store shelves. Like what the fuck?