some icons appears duplicate in gnome bookmarks in lateral bar when I open it. For example (in the figure) I have Kile as bookmark but when I open the software, a new icon appears in the bar. I think that should behave as the Chromium icon in the example (just with a “dot” on it).
Just a wild guess, maybe you have two copies of those apps, say one from openSUSE repos and another from upstream installed to /opt/… or remnants of a prior installation.
Try to take away the icon from the sidebar and then pinning it again making sure it is from the app you are actually using…
I have tried it. But for example, if I open Kile and try to pin it in bookmarks, there isn’t this option in the icon. If I want to do that I need to drag and drop the icon there, without open it.
You may look at what the actual configuration is, and see if anything odd shows up. For instance, for my favorite app “Firefox” I would open a terminal and type:
bruno@LT_B:~> gsettings get org.gnome.shell favorite-apps
'firefox.desktop', 'evolution.desktop', 'empathy.desktop', 'gnome-music.desktop', 'org.gnome.Nautilus.desktop']
bruno@LT_B:~> ls /usr/share/applications/firefox*
/usr/share/applications/firefox.desktop
bruno@LT_B:~> nano /usr/share/applications/firefox.desktop
and look for missing or duplicate launchers (xxx.desktop files) or strange details shown by the editor (nano or your favourite one)