This issue with ‘bookmark-fontify’ came up (within a broader
discussion) on the list in May, in particular by Bastien in
+message-id:<8735v0w5fv.fsf@bzg.fr>. It's obtrusive with the way
‘org-refile’ and ‘org-capture’ use bookmarks, but still bothersome
outside of org. It's not yet fixed in current master.

To reproduce, make sure ‘bookmark-fontify’ is t (the default in
master) and ‘bookmark-face’ is noticeable (orange background by
default). Then:

    emacs -Q
    ;; Visit any file with >20 lines, e.g.:
    M-x find-library RET bookmark RET
    ;; Set bookmark to current line
    C-x r m RET
    ;; Go elsewhere and overwrite same bookmark:
    C-u C-u C-n
    C-x r m RET

When we set or jump to a bookmark, that line gets fontified in the
buffer. Move down a few lines, and set the bookmark again with the
same name. This will (by default) overwrite the previous location, but
now *both* locations are displayed using bookmark-face. When a
bookmark is deleted with ‘bookmark-delete’ or within
‘bookmark-bmenu-list’ (C-x r l), its location gets unfontified. But
when just overwritten, the font overlay remains.

In the fix, I tried to split and edit the nearby comment for clarity
as well. Feedback welcome, thanks.

CL