I tried replicating what you describe and the boss triggered fine as normal so I am wondering if it may be due to a dodgy save file or something like that perhaps?
Tried again. My most recent save file loads in the dungeon, not far from the stairs. (Not downstairs with the crystal.) Took a screen clip of the crystal. The player is blocked from touching it from the front/the player can't get any closer than in the picture. I am playing the web version.