I can think of a few things that explain this:
1. some items do not have (or have lost) their icon. Check your inventory for an empty slot with a quantity number, and right-click to see the description
2. When you do not have empty slots in your inventory, the system automatically looks inside any sacks you have, and if it finds room there, stores the item in it. Check inside all sacks you have (including glyph sacks) to see if they are there.
3. For some reason you did not get them, because inventory was full. This should be shown in your system window though, so you probably would have noticed that.
I think the second is most likely.