Yes, I realize this is two years old, but I found another reason this might happen. There is no write up on any wiki or anything so, here is this submission:
For some reason the game will not recognize certain greater soul gems that you fill yourself. I am unsure of why, or whether there are only a few "greater" creature spawns that do this. (I came across this bug, specifically, by capturing the soul of the Wispmother by Winterhold.) This greater soul gem would not be accepted as an offering, though, another in my inventory was.
...Hands up in the air! Hallelujah!