There is a small room in the Luminous Labyrinth with what appears to be an altar and a mirror that, unlike the rest in the labyrinth, cannot be moved. Even if you manage to redirect all six of the beam colors to this room, nothing ever happens.
A clear outline of a trap door can be seen just outside the basement entrance in Owmi's Lord Manor, but at no point in any of the seven chapters does it actually open. Spoiler:There is an instance in Riki's chapter where you're dumped down a trap door in this very house, but that one is located underneath the symbol on the floor of the main hall.
A woman at the shrine in Devin will allow you to ask her about Time and Space magic. However, you can also ask her to "draw a sacred lot", to which she always responds that she's "sold out". This never changes at any point in any chapter, so there`s never any opportunity in the game to ever draw a sacred lot.
One of the rooms in Berva's underground base contains a number of mysteriously useless objects. First, the treasure chest here can not be opened. Upon trying to examine it, there's no message stating it's locked. It will simply not open, no matter what. Second, there's a strange-looking object here that is very clearly meant to stand out, but like the chest, absolutely nothing happens if it is examined. No effect or message appears at all. Finally, there are a pair of YellowFighters behind the wall in the middle of the room that you can't see, but can still fight. Odds are they would have jumped out at you after taking the chest or messing with the strange object, but as neither work, these enemies never show themselves.
Deep within the Koorong sewers exists a single manhole that won't open. Upon examining it, a message appears about the lid being stuck. However, there is no actual way of ever opening it up.
There is an image that flashes very briefly on the screen shortly after Asellus wakes up at the start of her chapter. The image is actuallySpoiler: the last memory Asellus had before her death and rebirth, as she was run over and killed by a carriage, and revived by a transfusion of mystic blood.