I KNOW there once was a topic about that. Sorry. I cannot find it in the now only 2 (!?) pages on this subforum. I don't know, if you staff guys want to address it, just mentioning it again, just in case.
So I have (had for a long time) various items in my vault, that exist in a big stack PLUS an extra single item next to it. I never had the time or patience to or was in the mood for dealing with any of those. Today I wanted to give items to the RB. One among those Fire Defense Tear Crystal. So I found, I had 932 in a stack and sitting next to them. Grabbing the opportunity, I removed the single one first before turning to the batch. Well, "clearing" that single item put one Crystal into my inventory, yet in vault it was replaced by one from the stack. Thus the double appearance still persists.