I wasn’t able to get a screenshot, but Ive had this happen twice now when I killed the boss of a NMD and the glyphstone was near a southern wall.
The obol chest typically spawns south of the glyphstone so I think if there’s just no room for it it doesn’t spawn.
Just happened to me in the Wretched delve in the Shamans lair boss room.
On a side note I’ve also seen the chest flying in midair. It was still clickable so just visual bug but pretty funny looking