Since Lucifer's Call was mentioned I'll mention my scariest and most annoying glitch in my copy. In the 3rd level of the Labyrinth (you know, the place where Dante breaks your nerves, but I mean slightly after that) there is a huge hallway at some point which leads to the 4th level - assuming you can open the doors and such. There, a certain combination of random encounter monsters appear that freeze my game. To get there means you have spend hours doing stuff without saving. Which can be super frustrating. And no matter how many times I tried, the only monster-team encounter I faced there was that certain one.
Thankfully I had one of those items that let you pass by places without meeting any monsters and this is what saved me. Each time I reply now, I carry like 10 of those..