I want to thank Darken for providing his feedback on the questions I recently posted. I was able to pinpoint the existing bugs reported by Darken, and provide a workaround for the time being. I'll fix it afterwards.
In the Catacombs, you might experience some problems with the Caterpillar System, de-syncing and whatnot. Simply go to the next room; that should fix it.
also, in the 1st basement, when you are trying to go up the stairs in the north section (To go back up to the 1st floor and move the plot on), you might encounter an error if you walk on the center or right tile of the stairs. Simply hug the left side of the stairs and move up. That should trigger the sequence.