I do this all the time because my inventory is full of charms
Pick up item on cursor and drop it into cube … then ID it. It logs item in chronicle correctly
Is this a bug that only happens rarely?
Rare, yes. But still a known bug and has happened more than enough times to where we figured out the cause of it. But it won't happen if you don't do it. But why risk it? Chances are it'll trigger on an item like tyraels and you'll be extremely annoyed.
Really all you have to do is stick your charms in cube once you find a drop and then pickup the item without putting it on your cursor first. You can avoid the glitch by doing that and without having to keep empty space in your inventory.