I want to keep this topic alive because I doubt it’s only happening to me, though it may go unnoticed by people who don’t have many (or any) duplicate bookmarks.
I just ran a search in Bookmark Manager. Five instances of the same URL (identical, no variation) turned up as results. Of these, three were shown (under “Show in folder”) as being in one bookmark folder and two were shown as being in another bookmark folder.
I opened both of these two bookmark folders. Each of them displayed only one instance of the bookmark.
This is something I’ve been seeing happening repeatedly.
My conclusion: Something is happening in the ‘search’ that is causing a single bookmark to identify multiple instances of itself, even though there is actually only one in each folder in which the search shows the bookmark as being located.
Either that or the duplication (or triplication, etc.) is for some reason not being shown when the folder is opened.