If I use the same filetype twice in the field "Include other files ... ! e.g. "*.jpg;*.jpg" in "Organize", then the file is listed twice in the restructuring result tree (with the same name).
After saving, for each file (which is listed double) appears the error message "file already exists".
It happend to me because I didn't pay attention.
It's rather less a bug then an information for the users which are probably as careless as me.
Organize - extensions listed double in Include other fiiles
Re: Organize - extensions listed double in Include other fii
Thanks for reporting, a fix is available in the current beta refresh