I'm playing through Shiori's path and I'm in the Stickers on Caskets chapter. At one point, an icon of what looks like a book with a small X on it drops in the top right corner of the screen. What does this indicate? It seems like an appropriate segment for a NSFW scene and I fear that icon means I missed it somehow? Thanks.

The game has sometimes unique dialogue that relies on player's attributes, affection points with X characters, played scenes, made choices, met characters and the like. What you described is a skill check behind Academics attribute. If you would meet a certain condition (in this case having a certain amount of Academics points), you would see an additional line. No need to worry, they are not designed to lock from experiencing core story or anything like that