I use the "notes" field as a final column in Zotero, to let me know at a glance when I have a note attached to an item even if the item entry is collapsed. I haven't seen it miss a note, but it has a fair number of false positives. What seems to happen is that it occasionally counts a phantom note as being attached to an attached file rather than to the parent item--which is not even possible. Any idea what information the counter might be picking up and counting as a note?